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Outline

One of the most important functionalities of OmicSelector is the ability to develop deep learning models. As OmicSelector focuses on biomarker feature selection and model development, it is one of the few solutions for developing deep feedforward neural networks (up to 3 hidden layers) with and without (sparse) autoencoder. OmicSelector provides both the framework and graphical interface to develop the best artificial neural network for molecular, laboratory, and clinical data. Please note, however, that OmicSelector was not designed to handle images or DICOM files. Multiple alternatives exist which handle imaging data.

Our solution’s primary purpose is to develop the best classification tool when a limited number of samples are available (e.g., expression data; due to cost). The researcher would like to create a classifier resilient to overfitting.

This extensions provides a unified pipeline which utilizes TensorFlow though Keras to create feedforward neural networks. OmicSelector, however, doesn’t require any knowledge of those technologies.

The extension needs to be loaded using:

OmicSelector::OmicSelector_load_extension("deeplearning")

This function loads the latest version of the extension from GitHub: https://github.com/kstawiski/OmicSelector/blob/master/extensions/deeplearning.R

OmicSelector_deep_learning function

This extension requires three datasets: training, testing, and validation datasets, as in Benchmarking (in standard OmicSelector pipeline). Those can be prepared using OmicSelector_prepare_split() or designed manually. The primary function for the training of neural networks is called OmicSelector_deep_learning(). This function aims to train several neural networks, test their performance, save models, and provide a general overview of the whole modeling.

OmicSelector_deep_learning() is defined with following parameters:

General setup parameters:

  • selected_miRNAs - a character vector of features of interest (selected features). The function will subset and train the networks only on those features.
  • wd - working directory where data files are to be found. In the working directory the function expects: mixed_train.csv (training set), mixed_test.csv (testing set), mixed_valid.csv (validation set). All files should contain binary Class variables (with values Case and Control) and features of interest (starting with prefix hsa).
  • SMOTE - logical parameter defining if the balanced training set should be used in the analysis. If set to FALSE, the function will use mixed_train.csv as a training set without any modification. If set to TRUE a balanced dataset will be used. Balancing is based on OmicSelector_load_datamix() function.
  • clean_temp_files - logical parameter defining if the temporary files (from directory temp-deeplearning) should be deleted after the function finishes. As best neural networks are saved in separate models directory, we advise keeping this TRUE. Setting it to FALSE may be useful in debugging.

Saving options:

  • save_threshold_trainacc - the threshold of training accuracy required for the model to be considered worth saving. Suppose set to 0.85, all models with training accuracy < 0.85 will be regarded as worthless and disregarded.
  • save_threshold_testacc - the threshold of testing accuracy required for the model to be considered as worth saving. Suppose set to 0.85, all models with testing accuracy < 0.85 will be regarded as worthless and disregarded.
  • add_features_to_predictions - logical parameter if the features should be added to predictions in model files. After the network is trained, the function checks the performance using the network for predictions in all 3 (training, testing, and validation) datasets. This may be useful for further analysis, but it will increase the final model zip files’ size. If you care about storage space, you should set it to FALSE.
  • output_file - the name of csv file used to save the results (hyperparameters and performance) of the training process. Without the extension (i.e. .csv) it also defines the name of the configuration.

Both training accuracy > save_threshold_trainacc and testing accuracy > save_threshold_testacc are required to consider the model useful. We did it to save storage space and do not save not working models. Please note, however, that the metrics of the models will be saved in output_file for further analysis.

Training control parameters:

  • keras_batch_size - Batch size is the number of training examples in one pass. The higher the batch size, the more memory space you’ll need.
  • keras_epochae - Maximum number of epoch (one forward pass and one backward pass of all the training examples) in the process of autoencoder training.
  • keras_epoch - Maximum number of epoch (one forward pass and one backward pass of all the training examples) in the process of final feedforward network training.
  • keras_patience - After how many epochs with no improvement in validation loss (loss on testing set) training should be stopped? See keras::callback_early_stopping() for more details.
  • keras_threads - This function allows you to make the training process parallel for different sets of hyperparameters. Depending on your hardware (CPU/GPU, memory, HDD/SDD speed etc.) and dataset size, you have to choose it individually. The value 2 is always safe, but it will mean that only two networks will be trained at the same time and for some presets, it may take an eternity to finish the process.

OmicSelector trains a defined number of epochs (assuming that early stopping criteria are not met), but the final network is the one with the lowest validation loss.

Hyperparameters (grid search):

Hyperparameters data frame contains the information about hyperparameter sets we want to check in grid search for the best model. You can play with the following hyperparameters:

  • layer1 - number of neurons in first hidden layer
  • layer2 - number of neurons in second hidden layer. If set to 0 = none.
  • layer3 - number of neurons in third hidden layer. If set to 0 = none.
  • activation_function_layer1 - activation function used in first hidden layer. Use names from: https://keras.io/api/layers/activations/
  • activation_function_layer2 - activation function used in second hidden layer. Use names from: https://keras.io/api/layers/activations/
  • activation_function_layer3 - activation function used in third hidden layer. Use names from: https://keras.io/api/layers/activations/
  • dropout_layer1 - dropout rate in first hidden layer. Dropout layer randomly sets input units to 0 with a frequency of rate at each step during training time, which helps prevent overfitting.
  • dropout_layer2 - dropout rate in second hidden layer.
  • dropout_layer3 - dropout rate in third hidden layer.
  • layer1_regularizer - if regularization should be used in the first hidden layer. We use L1 regularization and L1 regularization penalty of 0.001. Regularizers allow you to apply penalties on layer parameters or layer activity during optimization.
  • layer2_regularizer - if regularization should be used in the second hidden layer.
  • layer3_regularizer - if regularization should be used in the third hidden layer.
  • optimizer - use one of available optimizers (https://keras.io/api/optimizers/). We recommend adam.
  • autoencoder - if and with how many neurons the autoencoder should be used in structure network. If set to 0 - no autoencoder will be used, meaning that training features will go to the input layer directly. If set to >0, e.g. 4, the 5-layer autoencoder is created and deep features from autoencoder are used in the training of feedforward neural networks. In this scenario, the second hidden layer has a maximum of 7 neurons. The following bottleneck layer (deep features) has the number of neurons equal to the autoencoder parameter (4 in this example). If set to <0, e.g. -4 the similar autoencoder is created but L1 regulization (L1 regularization penalty of 0.001) is used in all hidden layers - creating sparse autoencoder. Autoencoders inherit other training parameters (e.g., optimizer; from the first layer of hyperparameter set).
  • balanced - if balanced training set should be used.
  • formula - formulas. We advise to create it using as.character(OmicSelector_create_formula(selected_miRNAs))[3].
  • scaled - if z-score should be applied to all datasets before modeling. Scaling can speed up and improve the process of training. Scaling parameters are calculated on the training set and reapplied on testing and validation sets.

If you do not want to check all hyperparameter sets (all rows in hyperparameters dataset):

  • start - from which row of hyperparameters data frame should we start?
  • end - at which row of hyperparameters data frame should we end?

You can use default values if you don’t know what to do. OmicSelector’s GUI uses default values set by us.

In OmicSelector’s GUI we use 3 presets of hyperparameters:

  • Quick scan (only the simple neural networks = with 1 hidden layer and without autoencoders; 1994 networks):
balanced = F  # not balanced
selected_miRNAs = c("hsa.a", "hsa.b", "hsa.c")  # selected features
hyperparameters = expand.grid(layer1 = seq(2, 10, by = 1), layer2 = c(0), layer3 = c(0), activation_function_layer1 = c("relu", "sigmoid", "selu"), activation_function_layer2 = c("relu"),
    activation_function_layer3 = c("relu"), dropout_layer1 = c(0, 0.1), dropout_layer2 = c(0), dropout_layer3 = c(0), layer1_regularizer = c(T, F), layer2_regularizer = c(F),
    layer3_regularizer = c(F), optimizer = c("adam", "rmsprop", "sgd"), autoencoder = c(0, -7, 7), balanced = balanced, formula = as.character(OmicSelector_create_formula(selected_miRNAs))[3],
    scaled = c(T, F), stringsAsFactors = F)
DT::datatable(hyperparameters, extensions = c("FixedColumns", "FixedHeader"), options = list(scrollX = TRUE, paging = TRUE))
  • Full scan (feedforward neural networks up to 3 hidden layers, without autoencoders; 97848 networks):
hyperparameters_part1 = expand.grid(layer1 = seq(2, 10, by = 1), layer2 = c(0), layer3 = c(0), activation_function_layer1 = c("relu", "sigmoid", "selu"),
    activation_function_layer2 = c("relu"), activation_function_layer3 = c("relu"), dropout_layer1 = c(0, 0.1), dropout_layer2 = c(0), dropout_layer3 = c(0),
    layer1_regularizer = c(T, F), layer2_regularizer = c(F), layer3_regularizer = c(F), optimizer = c("adam", "rmsprop", "sgd"), autoencoder = c(0), balanced = balanced,
    formula = as.character(OmicSelector_create_formula(selected_miRNAs))[3], scaled = c(T, F), stringsAsFactors = F)
hyperparameters_part2 = expand.grid(layer1 = seq(3, 11, by = 2), layer2 = c(seq(3, 11, by = 2)), layer3 = c(seq(0, 11, by = 2)), activation_function_layer1 = c("relu",
    "sigmoid", "selu"), activation_function_layer2 = c("relu", "sigmoid", "selu"), activation_function_layer3 = c("relu", "sigmoid", "selu"), dropout_layer1 = c(0,
    0.1), dropout_layer2 = c(0), dropout_layer3 = c(0), layer1_regularizer = c(T, F), layer2_regularizer = c(F), layer3_regularizer = c(F), optimizer = c("adam",
    "rmsprop", "sgd"), autoencoder = c(0), balanced = balanced, formula = as.character(OmicSelector_create_formula(selected_miRNAs))[3], scaled = c(T,
    F), stringsAsFactors = F)
hyperparameters = rbind(hyperparameters_part1, hyperparameters_part2)
  • Extended scan (feedforward neural networks up to 3 hidden layers, without autoencoders, with autoencoders and sparse autoencoders; 293544 networks)
hyperparameters_part1 = expand.grid(layer1 = seq(2, 10, by = 1), layer2 = c(0), layer3 = c(0), activation_function_layer1 = c("relu", "sigmoid", "selu"),
    activation_function_layer2 = c("relu"), activation_function_layer3 = c("relu"), dropout_layer1 = c(0, 0.1), dropout_layer2 = c(0), dropout_layer3 = c(0),
    layer1_regularizer = c(T, F), layer2_regularizer = c(F), layer3_regularizer = c(F), optimizer = c("adam", "rmsprop", "sgd"), autoencoder = c(0, -7,
        7), balanced = balanced, formula = as.character(OmicSelector_create_formula(selected_miRNAs))[3], scaled = c(T, F), stringsAsFactors = F)
hyperparameters_part2 = expand.grid(layer1 = seq(3, 11, by = 2), layer2 = c(seq(3, 11, by = 2)), layer3 = c(seq(0, 11, by = 2)), activation_function_layer1 = c("relu",
    "sigmoid", "selu"), activation_function_layer2 = c("relu", "sigmoid", "selu"), activation_function_layer3 = c("relu", "sigmoid", "selu"), dropout_layer1 = c(0,
    0.1), dropout_layer2 = c(0), dropout_layer3 = c(0), layer1_regularizer = c(T, F), layer2_regularizer = c(F), layer3_regularizer = c(F), optimizer = c("adam",
    "rmsprop", "sgd"), autoencoder = c(0, -7, 7), balanced = balanced, formula = as.character(OmicSelector_create_formula(selected_miRNAs))[3], scaled = c(T,
    F), stringsAsFactors = F)
hyperparameters = rbind(hyperparameters_part1, hyperparameters_part2)

The network’s standard training is regulated by the structure (defined by current hyperparameters). The data frame hyperparameters defines which hyperparameter sets are to be checked in the training process. This is a grid search, so every set of hyperparameters will be fit in this process.

The function starts with looking for the current working directory data (defined as wd). It expects the files to be named as mixed_train.csv (training set), mixed_test.csv (testing set), mixed_valid.csv (validation set). The file should contain binary Class variable (with values Case and Control) and features of interest (starting with prefix hsa). Neural networks are trained with early stopping. As the neural network is trained based on ROC analysis, the cutoff is being chosen. We use the cutoff with the maximum value of Youden index (Youden’s J statistic = sensitivity + specificity - 1). If the predicted probability is greater or equal to the cutoff, the case is predicted as Case. Otherwise, it is considered to be a Control.

Let’s create those files from TCGA data.

data("orginal_TCGA_data")
suppressWarnings(suppressMessages(library(dplyr)))
cancer_cases = filter(orginal_TCGA_data, primary_site == "Pancreas" & sample_type == "PrimaryTumor")
control_cases = filter(orginal_TCGA_data, sample_type == "SolidTissueNormal")
cancer_cases$Class = "Case"
control_cases$Class = "Control"
dataset = rbind(cancer_cases, control_cases)
ttpm = OmicSelector_counts_to_log10tpm(danex = dplyr::select(dataset, starts_with("hsa")), metadane = dplyr::select(dataset, -starts_with("hsa")), ids = dataset$sample,
    filtr = F, filtr_minimalcounts = 1, filtr_howmany = 0.01)
#> 
#> DGEList unfiltered object with TPM was saved as TPM_DGEList.rds.
#> Returned data are log10(TPM).
ttpm = as.data.frame(ttpm)
zero_var = which(apply(ttpm, 2, var) == 0)  #which have no variance
ttpm = ttpm[, -zero_var]
# Not run: DE = OmicSelector_differential_expression_ttest(ttpm_features = dplyr::select(dataset, starts_with('hsa')), classes = dataset$Class, mode
# = 'logtpm') significant = DE$miR[DE$`p-value Bonferroni`<0.05]
selected_miRNAs = make.names(c("hsa-miR-192-5p", "hsa-let-7g-5p", "hsa-let-7a-5p", "hsa-miR-194-5p", "hsa-miR-122-5p", "hsa-miR-340-5p", "hsa-miR-26b-5p"))  # some selected miRNAs
match(selected_miRNAs, colnames(ttpm))
#> [1]  87 167   1 251 180 337  43
# dataset = dataset[sample(1:nrow(dataset),200),] # sample 100 random cases to make it quicker
OmicSelector_table(table(dataset$Class), col.names = c("Class", "Number of cases"))
#> 
#>    Case Control 
#>     178     675
# For full analysis: merged = OmicSelector_prepare_split(metadane = dplyr::select(dataset, -starts_with('hsa')), ttpm = ttpm)

merged = OmicSelector_prepare_split(metadane = dplyr::select(dataset, -starts_with("hsa")), ttpm = dplyr::select(ttpm, selected_miRNAs))
#> 
#> Saved 3 sets as csv in working directory. Retruned mixed dataset.
knitr::kable(table(merged$Class, merged$mix))
test train valid
Case 36 107 35
Control 135 405 135

Let’s train just 5 neural networks with 1 hidden layer (for the sake of this quick tutorial):

SMOTE = F  # use unbalanced set
deep_learning_results = OmicSelector_deep_learning(selected_miRNAs = selected_miRNAs, start = 5, end = 10)  # use default set of hyperparameters and options
DT::datatable(deep_learning_results, extensions = c("FixedColumns", "FixedHeader"), options = list(scrollX = TRUE, paging = FALSE, fixedHeader = TRUE))

Deep learning results were also saved as deeplearning_results.csv. This file contains the following variables:

  • Hyperparameters (defined as descibed above): layer1, layer2, layer3, activation_function_layer1, activation_function_layer2, activation_function_layer3, dropout_layer1, dropout_layer2, dropout_layer3, layer1_regularizer, layer2_regularizer, layer3_regularizer, optimizer, autoencoder, balanced, formula, scaled
  • model_id - model ID for reference
  • training_AUC - area under the ROC curve in the training process.
  • cutoff - the threshold of predicted probability for predicting the Case (vs. Control). If predicted probability >= cutoff, then it is a Case.
  • training_AUC2 - same are training_AUC, but calculated using different package (for sanity check).
  • training_AUC_lower95CI - lower 95%CI of AUC ROC
  • training_AUC_upper95CI - upper 95%CI of AUC ROC
  • training_Accuracy - accuracy on the training set
  • training_Sensitivity - sensitivity on training set (Case as class of interest)
  • training_Specificity - specificity on training set
  • training_PPV - positive predictive value on training set
  • training_NPV - negative predicitve value on training set
  • training_F1 - F1-measure on training set
  • test_Accuracy - accuracy on testing set
  • test_Sensitivity - sensitivity on testing set
  • test_Specificity - specificity on testing set
  • test_PPV - PPV on testing set
  • test_NPV - NPV on testing set
  • test_F1 - F1-measure on testing set
  • valid_Accuracy - accuracy on validation set
  • valid_Sensitivity - sensitivity on validation set
  • valid_Specificity - specificity on validation set
  • valid_PPV - PPV on validation set
  • valid_NPV - NPV on validation set
  • valid_F1 - F1-measure on validation set
  • name - name of the model (including configuration name), if you add .zip suffix this will represent the model filename in models/ directory.
  • worth_saving - if it was worth_saving (i.e. is saved in models/ directory) or the performance was to low and was disregarded
  • training_time - training time of the model in seconds. [Please note that in parallel training this may be incorrect.]

We prefer to choose the best model based on the highest metaindex value. Metaindex is the average of all accuracy metrics (on training, testing, and validation sets), but the final decision is arbitrary.

Utilizing the networks for predictions

Deep neural networks created using OmicSelector can be used for prediction on new datasets using:

Input parameters:

  • model_path - path to the zip file with the networking created using OmicSelector
  • new_dataset - data frame with new data, must contain variables with the same names as predictors
  • new_scaling - if the network is scaled using z-score (in preprocessing), the function can restore scaling parameters from the training process (recommended) or create new scaling (useful when dealing with e.g. batch effect)
  • old_train_csv_to_restore_scaling - default to NULL; scaling parameters are saved in the model, but sometimes you may want to modify them. If you want to calculate scaling parameters based on some other dataset, please provide a path to the csv file.
  • override_cutoff - be default the predictions will be made based on predicted probability and cutoff (with highest Youden index in the training process; it remains constant between sets); if you do not want that, you can give your cutoff here
  • blinded - if your dataset contains the Class variable, you can set it to TRUE, and performance will be automatically calculated

Output (list):

  • predictions - data frame with predicted probabilites and classes
  • network_config - data frame with network configuration
  • new_dataset - data frame with new dataset for predictions (before preprocessing)
  • new_dataset_x - data frame with new dataset for predictions after preprocessing (scaling, deep features etc.)
  • network_features - features (variables, predictiors) in the network
  • cutoff - cutoff of predicted probability used in prediction
  • col_mean_train - if scaled network, mean values for every variable
  • col_sd_train - if scaled network, standard deviation values for every variable
  • confusion_matrix - confusion matrix (performance assessment)
  • roc - ROC curve (pROC object; can be used for plotting)
  • roc_auc - AUC ROC
  • model - model object (keras object)
  • autoencoder - autoencoder model object (keras object)

You can see the function working in the scoring tool inside OmicSelector’s GUI. If you are interested in code, look here.

Sesssion

sessionInfo()
#> R version 4.2.0 (2022-04-22)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.4 LTS
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#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
#> 
#> locale:
#>  [1] LC_CTYPE=C.UTF-8          LC_NUMERIC=C             
#>  [3] LC_TIME=C.UTF-8           LC_COLLATE=C.UTF-8       
#>  [5] LC_MONETARY=C.UTF-8       LC_MESSAGES=C.UTF-8      
#>  [7] LC_PAPER=C.UTF-8          LC_NAME=C.UTF-8          
#>  [9] LC_ADDRESS=C.UTF-8        LC_TELEPHONE=C.UTF-8     
#> [11] LC_MEASUREMENT=C.UTF-8    LC_IDENTIFICATION=C.UTF-8
#> 
#> attached base packages:
#> [1] grid      stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#>  [1] Biocomb_0.4        Rcpp_1.0.8.3       gtools_3.9.2.1    
#>  [4] rsq_2.5            edgeR_3.38.1       limma_3.52.1      
#>  [7] funModeling_1.9.4  Hmisc_4.7-0        Formula_1.2-4     
#> [10] forcats_0.5.1      purrr_0.3.4        readr_2.1.2       
#> [13] tidyr_1.2.0        tibble_3.1.7       tidyverse_1.3.1   
#> [16] data.table_1.14.2  stringr_1.4.0      devtools_2.4.3    
#> [19] usethis_2.1.6      gplots_3.1.3       gridExtra_2.3     
#> [22] ROSE_0.0-4         DMwR_0.4.1         pROC_1.18.0       
#> [25] epiDisplay_3.5.0.2 nnet_7.3-17        MASS_7.3-57       
#> [28] survival_3.2-13    foreign_0.8-82     caret_6.0-92      
#> [31] lattice_0.20-45    ggplot2_3.3.6      plyr_1.8.7        
#> [34] OmicSelector_1.0.0 dplyr_1.0.9        BiocStyle_2.24.0  
#> 
#> loaded via a namespace (and not attached):
#>   [1] utf8_1.2.2           tidyselect_1.1.2     lme4_1.1-29         
#>   [4] htmlwidgets_1.5.4    munsell_0.5.0        codetools_0.2-18    
#>   [7] ragg_1.2.2           DT_0.23              future_1.26.1       
#>  [10] withr_2.5.0          colorspace_2.0-3     highr_0.9           
#>  [13] knitr_1.39           rstudioapi_0.13      stats4_4.2.0        
#>  [16] ROCR_1.0-11          rJava_1.0-6          TTR_0.24.3          
#>  [19] listenv_0.8.0        rprojroot_2.0.3      parallelly_1.31.1   
#>  [22] vctrs_0.4.1          generics_0.1.2       ipred_0.9-12        
#>  [25] xfun_0.31            randomForest_4.7-1.1 R6_2.5.1            
#>  [28] doParallel_1.0.17    locfit_1.5-9.5       bitops_1.0-7        
#>  [31] cachem_1.0.6         assertthat_0.2.1     scales_1.2.0        
#>  [34] gtable_0.3.0         globals_0.15.0       processx_3.5.3      
#>  [37] timeDate_3043.102    rlang_1.0.2          systemfonts_1.0.4   
#>  [40] pamr_1.56.1          splines_4.2.0        lazyeval_0.2.2      
#>  [43] ModelMetrics_1.2.2.2 broom_0.8.0          checkmate_2.1.0     
#>  [46] rgl_0.108.3.2        BiocManager_1.30.18  yaml_2.3.5          
#>  [49] reshape2_1.4.4       abind_1.4-5          modelr_0.1.8        
#>  [52] crosstalk_1.2.0      backports_1.4.1      quantmod_0.4.20     
#>  [55] tools_4.2.0          lava_1.6.10          bookdown_0.26       
#>  [58] ellipsis_0.3.2       jquerylib_0.1.4      RColorBrewer_1.1-3  
#>  [61] proxy_0.4-26         sessioninfo_1.2.2    base64enc_0.1-3     
#>  [64] ps_1.7.0             prettyunits_1.1.1    rpart_4.1.16        
#>  [67] zoo_1.8-10           haven_2.5.0          cluster_2.1.3       
#>  [70] fs_1.5.2             magrittr_2.0.3       reprex_2.0.1        
#>  [73] RWeka_0.4-44         pkgload_1.2.4        hms_1.1.1           
#>  [76] evaluate_0.15        jpeg_0.1-9           readxl_1.4.0        
#>  [79] testthat_3.1.4       compiler_4.2.0       KernSmooth_2.23-20  
#>  [82] crayon_1.5.1         minqa_1.2.4          htmltools_0.5.2     
#>  [85] entropy_1.3.1        tzdb_0.3.0           snow_0.4-4          
#>  [88] lubridate_1.8.0      DBI_1.1.2            formatR_1.12        
#>  [91] dbplyr_2.1.1         arules_1.7-3         boot_1.3-28         
#>  [94] Matrix_1.4-1         brio_1.1.3           cli_3.3.0           
#>  [97] parallel_4.2.0       gower_1.0.0          pkgconfig_2.0.3     
#> [100] pkgdown_2.0.3        recipes_0.2.0        xml2_1.3.3          
#> [103] foreach_1.5.2        bslib_0.3.1          hardhat_0.2.0       
#> [106] RWekajars_3.9.3-2    prodlim_2019.11.13   rvest_1.0.2         
#> [109] callr_3.7.0          digest_0.6.29        rmarkdown_2.14      
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#> [124] httr_1.4.3           pkgbuild_1.3.1       glue_1.6.2          
#> [127] xts_0.12.1           remotes_2.4.2        png_0.1-7           
#> [130] iterators_1.0.14     pander_0.6.5         class_7.3-20        
#> [133] stringi_1.7.6        sass_0.4.1           moments_0.14.1      
#> [136] textshaping_0.3.6    FSelector_0.33       latticeExtra_0.6-29 
#> [139] caTools_1.18.2       memoise_2.0.1        e1071_1.7-9         
#> [142] future.apply_1.9.0
packageDescription("OmicSelector")
#> Package: OmicSelector
#> Type: Package
#> Title: OmicSelector - a package for biomarker selection based on
#>        high-throughput experiments.
#> Version: 1.0.0
#> Author: Konrad Stawiski
#> Maintainer: Konrad Stawiski <konrad.stawiski@umed.lodz.pl>
#> Description: OmicSelector is package is the environment,
#>        docker-based application and R package for biomarker
#>        signature selection from high-throughput experiments.
#>        Initially developed for miRNA-seq. The package introduces
#>        automatic and structured feature selection with further
#>        benchmarking using multiple data mining methods, thus
#>        allow to find the most overfitting resiliant signature
#>        (set of featrues) that can be used in biomarker validation
#>        studies. E.g. this package can be used to find the set of
#>        miRNAs with the greatest biomarker potential based on
#>        miRNAs-seq. This set can be further validated in cheaper
#>        qPCR studies.
#> License: License: MIT + file LICENSE
#> Encoding: UTF-8
#> LazyData: true
#> Suggests: knitr, rmarkdown
#> VignetteBuilder: knitr
#> StagedInstall: yes
#> Imports: dplyr, snow, remotes, devtools, ellipsis, BiocManager,
#>        plyr, tibble, tidyr, XML, epiDisplay, rsq, MASS, caret,
#>        tidyverse, xtable, pROC, ggplot2, DMwR, ROSE, gridExtra,
#>        gplots, stringr, data.table, doParallel, Boruta, spFSR,
#>        varSelRF, My.stepwise, psych, C50, randomForest, nnet,
#>        reticulate, stargazer, ggrepel, classInt, plotly, keras,
#>        cutpointr, naniar, visdat, imputeMissings, foreach,
#>        deepnet, calibrate, networkD3, VennDiagram, RSNNS,
#>        kernlab, car, PairedData, profileR, xgboost, kableExtra,
#>        curl, tidyselect, rJava, mice, MatchIt, cluster, Biobase,
#>        Biocomb, ComplexHeatmap, GDCRNATools, R.utils,
#>        TCGAbiolinks, VIM, circlize, edgeR, magick, mgcv, party,
#>        rmarkdown, rpart, sva, devtools, nnet, klaR,
#>        ParBayesianOptimization, recipes, resample, mlbench
#> RoxygenNote: 7.2.0
#> Authors@R: c( person("Konrad", "Stawiski", ,
#>        "konrad.stawiski@umed.lodz.pl", role = c("aut", "cre"),
#>        comment = c(ORCID = "0000-0002-6550-3384") ),
#>        person("Marcin", "Kaszkowiak", role = "aut"))
#> BugReports: https://github.com/kstawiski/OmicSelector/issues
#> URL: https://biostat.umed.pl/OmicSelector/
#> biocViews: Software
#> Depends: R (>= 2.10)
#> RemoteType: github
#> RemoteHost: api.github.com
#> RemoteRepo: OmicSelector
#> RemoteUsername: kstawiski
#> RemoteRef: HEAD
#> RemoteSha: 38c51527b9717cef4d7c5fe19e1a33b78ade494d
#> GithubRepo: OmicSelector
#> GithubUsername: kstawiski
#> GithubRef: HEAD
#> GithubSHA1: 38c51527b9717cef4d7c5fe19e1a33b78ade494d
#> NeedsCompilation: no
#> Packaged: 2022-06-01 20:44:34 UTC; konrad
#> Built: R 4.2.0; ; 2022-06-01 20:44:37 UTC; unix
#> 
#> -- File: /home/konrad/R/x86_64-pc-linux-gnu-library/4.2/OmicSelector/Meta/package.rds

To render this tutorial we used:

render("DeepLearningTutorial.Rmd", output_file = "DeepLearningTutorial.html", output_dir = "../inst/doc/")

Packages installed in our docker enviorment:

OmicSelector_table(as.data.frame(installed.packages()))
#>                                         Package
#> abind                                     abind
#> affy                                       affy
#> affyio                                   affyio
#> annotate                               annotate
#> AnnotationDbi                     AnnotationDbi
#> ape                                         ape
#> aplot                                     aplot
#> arm                                         arm
#> arules                                   arules
#> askpass                                 askpass
#> assertthat                           assertthat
#> autokeras                             autokeras
#> backports                             backports
#> base64enc                             base64enc
#> BBmisc                                   BBmisc
#> BH                                           BH
#> Biobase                                 Biobase
#> BiocCheck                             BiocCheck
#> BiocFileCache                     BiocFileCache
#> BiocGenerics                       BiocGenerics
#> BiocManager                         BiocManager
#> Biocomb                                 Biocomb
#> BiocParallel                       BiocParallel
#> BiocStyle                             BiocStyle
#> BiocVersion                         BiocVersion
#> biocViews                             biocViews
#> biomaRt                                 biomaRt
#> Biostrings                           Biostrings
#> bit                                         bit
#> bit64                                     bit64
#> bitops                                   bitops
#> blob                                       blob
#> bookdown                               bookdown
#> Boruta                                   Boruta
#> bounceR                                 bounceR
#> brew                                       brew
#> brio                                       brio
#> broom                                     broom
#> broom.helpers                     broom.helpers
#> bslib                                     bslib
#> C50                                         C50
#> cachem                                   cachem
#> calibrate                             calibrate
#> callr                                     callr
#> car                                         car
#> carData                                 carData
#> caret                                     caret
#> caTools                                 caTools
#> cellranger                           cellranger
#> checkmate                             checkmate
#> circlize                               circlize
#> classInt                               classInt
#> cli                                         cli
#> clipr                                     clipr
#> clue                                       clue
#> clusterProfiler                 clusterProfiler
#> coda                                       coda
#> coin                                       coin
#> colorspace                           colorspace
#> combinat                               combinat
#> commonmark                           commonmark
#> ComplexHeatmap                   ComplexHeatmap
#> config                                   config
#> corrplot                               corrplot
#> cowplot                                 cowplot
#> cpp11                                     cpp11
#> crayon                                   crayon
#> credentials                         credentials
#> crosstalk                             crosstalk
#> cubature                               cubature
#> Cubist                                   Cubist
#> curl                                       curl
#> cutpointr                             cutpointr
#> data.table                           data.table
#> DBI                                         DBI
#> dbplyr                                   dbplyr
#> dbscan                                   dbscan
#> deepnet                                 deepnet
#> DelayedArray                       DelayedArray
#> DEoptimR                               DEoptimR
#> Deriv                                     Deriv
#> desc                                       desc
#> DESeq2                                   DESeq2
#> devtools                               devtools
#> DiceKriging                         DiceKriging
#> diffobj                                 diffobj
#> digest                                   digest
#> DMwR                                       DMwR
#> DO.db                                     DO.db
#> doParallel                           doParallel
#> DOSE                                       DOSE
#> downlit                                 downlit
#> downloader                           downloader
#> dplyr                                     dplyr
#> DT                                           DT
#> dtplyr                                   dtplyr
#> e1071                                     e1071
#> edgeR                                     edgeR
#> ellipsis                               ellipsis
#> enrichplot                           enrichplot
#> entropy                                 entropy
#> epiDisplay                           epiDisplay
#> evaluate                               evaluate
#> exactRankTests                   exactRankTests
#> fansi                                     fansi
#> farver                                   farver
#> fastmap                                 fastmap
#> fastmatch                             fastmatch
#> feseR                                     feseR
#> fgsea                                     fgsea
#> filelock                               filelock
#> fontawesome                         fontawesome
#> forcats                                 forcats
#> foreach                                 foreach
#> formatR                                 formatR
#> Formula                                 Formula
#> fs                                           fs
#> FSelector                             FSelector
#> funModeling                         funModeling
#> furrr                                     furrr
#> futile.logger                     futile.logger
#> futile.options                   futile.options
#> future                                   future
#> future.apply                       future.apply
#> gargle                                   gargle
#> gdata                                     gdata
#> GDCRNATools                         GDCRNATools
#> genefilter                           genefilter
#> geneplotter                         geneplotter
#> generics                               generics
#> GenomeInfoDb                       GenomeInfoDb
#> GenomeInfoDbData               GenomeInfoDbData
#> GenomicDataCommons           GenomicDataCommons
#> GenomicRanges                     GenomicRanges
#> gert                                       gert
#> GetoptLong                           GetoptLong
#> ggbiplot                               ggbiplot
#> ggforce                                 ggforce
#> ggfun                                     ggfun
#> ggplot2                                 ggplot2
#> ggplotify                             ggplotify
#> ggpubr                                   ggpubr
#> ggraph                                   ggraph
#> ggrepel                                 ggrepel
#> ggsci                                     ggsci
#> ggsignif                               ggsignif
#> ggtext                                   ggtext
#> ggtree                                   ggtree
#> gh                                           gh
#> gitcreds                               gitcreds
#> gld                                         gld
#> glmnet                                   glmnet
#> GlobalOptions                     GlobalOptions
#> globals                                 globals
#> glue                                       glue
#> gmodels                                 gmodels
#> GO.db                                     GO.db
#> googledrive                         googledrive
#> googlesheets4                     googlesheets4
#> GOSemSim                               GOSemSim
#> gower                                     gower
#> gplots                                   gplots
#> graph                                     graph
#> graphlayouts                       graphlayouts
#> gridExtra                             gridExtra
#> gridGraphics                       gridGraphics
#> gridtext                               gridtext
#> gt                                           gt
#> gtable                                   gtable
#> gtools                                   gtools
#> gtsummary                             gtsummary
#> hardhat                                 hardhat
#> hash                                       hash
#> haven                                     haven
#> here                                       here
#> highr                                     highr
#> Hmisc                                     Hmisc
#> hms                                         hms
#> htmlTable                             htmlTable
#> htmltools                             htmltools
#> htmlwidgets                         htmlwidgets
#> HTqPCR                                   HTqPCR
#> httpuv                                   httpuv
#> httr                                       httr
#> ids                                         ids
#> igraph                                   igraph
#> imputeMissings                   imputeMissings
#> ini                                         ini
#> inum                                       inum
#> ipred                                     ipred
#> IRanges                                 IRanges
#> isoband                                 isoband
#> iterators                             iterators
#> jpeg                                       jpeg
#> jquerylib                             jquerylib
#> jsonlite                               jsonlite
#> kableExtra                           kableExtra
#> KEGGgraph                             KEGGgraph
#> KEGGREST                               KEGGREST
#> keras                                     keras
#> kernlab                                 kernlab
#> klaR                                       klaR
#> km.ci                                     km.ci
#> KMsurv                                   KMsurv
#> knitr                                     knitr
#> labeling                               labeling
#> labelled                               labelled
#> laeken                                   laeken
#> lambda.r                               lambda.r
#> later                                     later
#> latticeExtra                       latticeExtra
#> lava                                       lava
#> lavaan                                   lavaan
#> lazyeval                               lazyeval
#> lhs                                         lhs
#> libcoin                                 libcoin
#> lifecycle                             lifecycle
#> limma                                     limma
#> listenv                                 listenv
#> lme4                                       lme4
#> lmom                                       lmom
#> lmtest                                   lmtest
#> lobstr                                   lobstr
#> locfit                                   locfit
#> lubridate                             lubridate
#> magick                                   magick
#> magrittr                               magrittr
#> maptools                               maptools
#> markdown                               markdown
#> MatchIt                                 MatchIt
#> MatrixGenerics                   MatrixGenerics
#> MatrixModels                       MatrixModels
#> matrixStats                         matrixStats
#> maxstat                                 maxstat
#> mboost                                   mboost
#> memoise                                 memoise
#> mice                                       mice
#> mime                                       mime
#> miniUI                                   miniUI
#> minqa                                     minqa
#> mitools                                 mitools
#> mlbench                                 mlbench
#> mlr                                         mlr
#> mnormt                                   mnormt
#> ModelMetrics                       ModelMetrics
#> modelr                                   modelr
#> modeltools                           modeltools
#> moments                                 moments
#> mRMRe                                     mRMRe
#> multcomp                               multcomp
#> munsell                                 munsell
#> mvtnorm                                 mvtnorm
#> My.stepwise                         My.stepwise
#> naniar                                   naniar
#> networkD3                             networkD3
#> nloptr                                   nloptr
#> nnls                                       nnls
#> nondetects                           nondetects
#> norm                                       norm
#> np                                           np
#> numDeriv                               numDeriv
#> OmicSelector                       OmicSelector
#> openssl                                 openssl
#> org.Hs.eg.db                       org.Hs.eg.db
#> PairedData                           PairedData
#> pamr                                       pamr
#> pander                                   pander
#> parallelly                           parallelly
#> parallelMap                         parallelMap
#> ParamHelpers                       ParamHelpers
#> ParBayesianOptimization ParBayesianOptimization
#> parsetools                           parsetools
#> party                                     party
#> partykit                               partykit
#> patchwork                             patchwork
#> pathview                               pathview
#> pbivnorm                               pbivnorm
#> pbkrtest                               pbkrtest
#> pillar                                   pillar
#> pkgbuild                               pkgbuild
#> pkgcond                                 pkgcond
#> pkgconfig                             pkgconfig
#> pkgdown                                 pkgdown
#> pkgload                                 pkgload
#> plogr                                     plogr
#> plotly                                   plotly
#> plyr                                       plyr
#> png                                         png
#> polspline                             polspline
#> polyclip                               polyclip
#> polynom                                 polynom
#> postlogic                             postlogic
#> praise                                   praise
#> preprocessCore                   preprocessCore
#> prettyunits                         prettyunits
#> pROC                                       pROC
#> processx                               processx
#> prodlim                                 prodlim
#> profileR                               profileR
#> progress                               progress
#> progressr                             progressr
#> promises                               promises
#> proxy                                     proxy
#> pryr                                       pryr
#> ps                                           ps
#> psych                                     psych
#> purrr                                     purrr
#> purrrogress                         purrrogress
#> quadprog                               quadprog
#> quantmod                               quantmod
#> quantreg                               quantreg
#> questionr                             questionr
#> qvalue                                   qvalue
#> R.cache                                 R.cache
#> R.methodsS3                         R.methodsS3
#> R.oo                                       R.oo
#> R.utils                                 R.utils
#> R6                                           R6
#> ragg                                       ragg
#> randomForest                       randomForest
#> ranger                                   ranger
#> RANN                                       RANN
#> rappdirs                               rappdirs
#> rapportools                         rapportools
#> RBGL                                       RBGL
#> rcmdcheck                             rcmdcheck
#> RColorBrewer                       RColorBrewer
#> Rcpp                                       Rcpp
#> RcppArmadillo                     RcppArmadillo
#> RcppEigen                             RcppEigen
#> RcppProgress                       RcppProgress
#> RcppTOML                               RcppTOML
#> RCurl                                     RCurl
#> readr                                     readr
#> readxl                                   readxl
#> recipes                                 recipes
#> rematch                                 rematch
#> rematch2                               rematch2
#> remotes                                 remotes
#> reprex                                   reprex
#> resample                               resample
#> reshape                                 reshape
#> reshape2                               reshape2
#> reticulate                           reticulate
#> rgl                                         rgl
#> Rgraphviz                             Rgraphviz
#> rhandsontable                     rhandsontable
#> rJava                                     rJava
#> rjson                                     rjson
#> rlang                                     rlang
#> rmarkdown                             rmarkdown
#> rms                                         rms
#> robustbase                           robustbase
#> ROCR                                       ROCR
#> ROSE                                       ROSE
#> roxygen2                               roxygen2
#> rprojroot                             rprojroot
#> RSNNS                                     RSNNS
#> rsq                                         rsq
#> RSQLite                                 RSQLite
#> rstatix                                 rstatix
#> rstudioapi                           rstudioapi
#> RUnit                                     RUnit
#> rversions                             rversions
#> rvest                                     rvest
#> RWeka                                     RWeka
#> RWekajars                             RWekajars
#> S4Vectors                             S4Vectors
#> sandwich                               sandwich
#> sass                                       sass
#> scales                                   scales
#> scatterpie                           scatterpie
#> selectr                                 selectr
#> sessioninfo                         sessioninfo
#> shadowtext                           shadowtext
#> shape                                     shape
#> shiny                                     shiny
#> shinyfullscreen                 shinyfullscreen
#> shinyjqui                             shinyjqui
#> shinyjs                                 shinyjs
#> snow                                       snow
#> sourcetools                         sourcetools
#> sp                                           sp
#> SparseM                                 SparseM
#> spFSR                                     spFSR
#> SQUAREM                                 SQUAREM
#> stabs                                     stabs
#> stargazer                             stargazer
#> stringdist                           stringdist
#> stringi                                 stringi
#> stringr                                 stringr
#> strucchange                         strucchange
#> styler                                   styler
#> SummarizedExperiment       SummarizedExperiment
#> summarytools                       summarytools
#> survey                                   survey
#> survminer                             survminer
#> survMisc                               survMisc
#> sva                                         sva
#> svglite                                 svglite
#> sys                                         sys
#> systemfonts                         systemfonts
#> tableone                               tableone
#> TCGAbiolinks                       TCGAbiolinks
#> TCGAbiolinksGUI.data       TCGAbiolinksGUI.data
#> tensorflow                           tensorflow
#> testextra                             testextra
#> testthat                               testthat
#> textshaping                         textshaping
#> tfautograph                         tfautograph
#> tfruns                                   tfruns
#> TH.data                                 TH.data
#> tibble                                   tibble
#> tictoc                                   tictoc
#> tidygraph                             tidygraph
#> tidyr                                     tidyr
#> tidyselect                           tidyselect
#> tidytemplate                       tidytemplate
#> tidytree                               tidytree
#> tidyverse                             tidyverse
#> timeDate                               timeDate
#> tinytex                                 tinytex
#> tmvnsim                                 tmvnsim
#> treeio                                   treeio
#> TTR                                         TTR
#> tweenr                                   tweenr
#> tzdb                                       tzdb
#> UpSetR                                   UpSetR
#> usethis                                 usethis
#> utf8                                       utf8
#> uuid                                       uuid
#> varSelRF                               varSelRF
#> vcd                                         vcd
#> vctrs                                     vctrs
#> VennDiagram                         VennDiagram
#> VIM                                         VIM
#> viridis                                 viridis
#> viridisLite                         viridisLite
#> visdat                                   visdat
#> vroom                                     vroom
#> waiter                                   waiter
#> waldo                                     waldo
#> webshot                                 webshot
#> whisker                                 whisker
#> withr                                     withr
#> xfun                                       xfun
#> xgboost                                 xgboost
#> xlsx                                       xlsx
#> xlsxjars                               xlsxjars
#> XML                                         XML
#> xml2                                       xml2
#> xopen                                     xopen
#> xtable                                   xtable
#> xts                                         xts
#> XVector                                 XVector
#> yaml                                       yaml
#> yulab.utils                         yulab.utils
#> zeallot                                 zeallot
#> zip                                         zip
#> zlibbioc                               zlibbioc
#> zoo                                         zoo
#> base                                       base
#> boot                                       boot
#> class                                     class
#> cluster                                 cluster
#> codetools                             codetools
#> compiler                               compiler
#> datasets                               datasets
#> foreign                                 foreign
#> graphics                               graphics
#> grDevices                             grDevices
#> grid                                       grid
#> KernSmooth                           KernSmooth
#> lattice                                 lattice
#> MASS                                       MASS
#> Matrix                                   Matrix
#> methods                                 methods
#> mgcv                                       mgcv
#> nlme                                       nlme
#> nnet                                       nnet
#> parallel                               parallel
#> rpart                                     rpart
#> spatial                                 spatial
#> splines                                 splines
#> stats                                     stats
#> stats4                                   stats4
#> survival                               survival
#> tcltk                                     tcltk
#> tools                                     tools
#> utils                                     utils
#>                                                                LibPath
#> abind                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> affy                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> affyio                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> annotate                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> AnnotationDbi           /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ape                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> aplot                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> arm                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> arules                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> askpass                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> assertthat              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> autokeras               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> backports               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> base64enc               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> BBmisc                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> BH                      /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> Biobase                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> BiocCheck               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> BiocFileCache           /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> BiocGenerics            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> BiocManager             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> Biocomb                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> BiocParallel            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> BiocStyle               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> BiocVersion             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> biocViews               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> biomaRt                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> Biostrings              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> bit                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> bit64                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> bitops                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> blob                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> bookdown                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> Boruta                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> bounceR                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> brew                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> brio                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> broom                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> broom.helpers           /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> bslib                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> C50                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> cachem                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> calibrate               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> callr                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> car                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> carData                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> caret                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> caTools                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> cellranger              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> checkmate               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> circlize                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> classInt                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> cli                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> clipr                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> clue                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> clusterProfiler         /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> coda                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> coin                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> colorspace              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> combinat                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> commonmark              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ComplexHeatmap          /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> config                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> corrplot                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> cowplot                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> cpp11                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> crayon                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> credentials             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> crosstalk               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> cubature                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> Cubist                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> curl                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> cutpointr               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> data.table              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> DBI                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> dbplyr                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> dbscan                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> deepnet                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> DelayedArray            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> DEoptimR                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> Deriv                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> desc                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> DESeq2                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> devtools                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> DiceKriging             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> diffobj                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> digest                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> DMwR                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> DO.db                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> doParallel              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> DOSE                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> downlit                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> downloader              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> dplyr                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> DT                      /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> dtplyr                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> e1071                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> edgeR                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ellipsis                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> enrichplot              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> entropy                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> epiDisplay              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> evaluate                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> exactRankTests          /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> fansi                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> farver                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> fastmap                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> fastmatch               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> feseR                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> fgsea                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> filelock                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> fontawesome             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> forcats                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> foreach                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> formatR                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> Formula                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> fs                      /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> FSelector               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> funModeling             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> furrr                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> futile.logger           /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> futile.options          /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> future                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> future.apply            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> gargle                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> gdata                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> GDCRNATools             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> genefilter              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> geneplotter             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> generics                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> GenomeInfoDb            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> GenomeInfoDbData        /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> GenomicDataCommons      /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> GenomicRanges           /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> gert                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> GetoptLong              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ggbiplot                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ggforce                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ggfun                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ggplot2                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ggplotify               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ggpubr                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ggraph                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ggrepel                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ggsci                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ggsignif                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ggtext                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ggtree                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> gh                      /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> gitcreds                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> gld                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> glmnet                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> GlobalOptions           /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> globals                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> glue                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> gmodels                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> GO.db                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> googledrive             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> googlesheets4           /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> GOSemSim                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> gower                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> gplots                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> graph                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> graphlayouts            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> gridExtra               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> gridGraphics            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> gridtext                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> gt                      /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> gtable                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> gtools                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> gtsummary               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> hardhat                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> hash                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> haven                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> here                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> highr                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> Hmisc                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> hms                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> htmlTable               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> htmltools               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> htmlwidgets             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> HTqPCR                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> httpuv                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> httr                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ids                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> igraph                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> imputeMissings          /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ini                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> inum                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ipred                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> IRanges                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> isoband                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> iterators               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> jpeg                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> jquerylib               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> jsonlite                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> kableExtra              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> KEGGgraph               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> KEGGREST                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> keras                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> kernlab                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> klaR                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> km.ci                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> KMsurv                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> knitr                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> labeling                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> labelled                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> laeken                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> lambda.r                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> later                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> latticeExtra            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> lava                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> lavaan                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> lazyeval                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> lhs                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> libcoin                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> lifecycle               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> limma                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> listenv                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> lme4                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> lmom                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> lmtest                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> lobstr                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> locfit                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> lubridate               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> magick                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> magrittr                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> maptools                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> markdown                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> MatchIt                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> MatrixGenerics          /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> MatrixModels            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> matrixStats             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> maxstat                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> mboost                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> memoise                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> mice                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> mime                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> miniUI                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> minqa                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> mitools                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> mlbench                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> mlr                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> mnormt                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ModelMetrics            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> modelr                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> modeltools              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> moments                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> mRMRe                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> multcomp                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> munsell                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> mvtnorm                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> My.stepwise             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> naniar                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> networkD3               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> nloptr                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> nnls                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> nondetects              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> norm                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> np                      /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> numDeriv                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> OmicSelector            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> openssl                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> org.Hs.eg.db            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> PairedData              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> pamr                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> pander                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> parallelly              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> parallelMap             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ParamHelpers            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ParBayesianOptimization /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> parsetools              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> party                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> partykit                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> patchwork               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> pathview                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> pbivnorm                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> pbkrtest                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> pillar                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> pkgbuild                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> pkgcond                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> pkgconfig               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> pkgdown                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> pkgload                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> plogr                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> plotly                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> plyr                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> png                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> polspline               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> polyclip                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> polynom                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> postlogic               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> praise                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> preprocessCore          /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> prettyunits             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> pROC                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> processx                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> prodlim                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> profileR                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> progress                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> progressr               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> promises                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> proxy                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> pryr                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ps                      /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> psych                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> purrr                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> purrrogress             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> quadprog                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> quantmod                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> quantreg                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> questionr               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> qvalue                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> R.cache                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> R.methodsS3             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> R.oo                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> R.utils                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> R6                      /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ragg                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> randomForest            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ranger                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> RANN                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> rappdirs                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> rapportools             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> RBGL                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> rcmdcheck               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> RColorBrewer            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> Rcpp                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> RcppArmadillo           /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> RcppEigen               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> RcppProgress            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> RcppTOML                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> RCurl                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> readr                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> readxl                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> recipes                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> rematch                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> rematch2                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> remotes                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> reprex                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> resample                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> reshape                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> reshape2                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> reticulate              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> rgl                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> Rgraphviz               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> rhandsontable           /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> rJava                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> rjson                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> rlang                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> rmarkdown               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> rms                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> robustbase              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ROCR                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> ROSE                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> roxygen2                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> rprojroot               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> RSNNS                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> rsq                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> RSQLite                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> rstatix                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> rstudioapi              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> RUnit                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> rversions               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> rvest                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> RWeka                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> RWekajars               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> S4Vectors               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> sandwich                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> sass                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> scales                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> scatterpie              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> selectr                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> sessioninfo             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> shadowtext              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> shape                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> shiny                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> shinyfullscreen         /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> shinyjqui               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> shinyjs                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> snow                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> sourcetools             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> sp                      /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> SparseM                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> spFSR                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> SQUAREM                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> stabs                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> stargazer               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> stringdist              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> stringi                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> stringr                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> strucchange             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> styler                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> SummarizedExperiment    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> summarytools            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> survey                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> survminer               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> survMisc                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> sva                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> svglite                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> sys                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> systemfonts             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> tableone                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> TCGAbiolinks            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> TCGAbiolinksGUI.data    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> tensorflow              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> testextra               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> testthat                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> textshaping             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> tfautograph             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> tfruns                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> TH.data                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> tibble                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> tictoc                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> tidygraph               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> tidyr                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> tidyselect              /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> tidytemplate            /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> tidytree                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> tidyverse               /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> timeDate                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> tinytex                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> tmvnsim                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> treeio                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> TTR                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> tweenr                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> tzdb                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> UpSetR                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> usethis                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> utf8                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> uuid                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> varSelRF                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> vcd                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> vctrs                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> VennDiagram             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> VIM                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> viridis                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> viridisLite             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> visdat                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> vroom                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> waiter                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> waldo                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> webshot                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> whisker                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> withr                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> xfun                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> xgboost                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> xlsx                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> xlsxjars                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> XML                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> xml2                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> xopen                   /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> xtable                  /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> xts                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> XVector                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> yaml                    /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> yulab.utils             /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> zeallot                 /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> zip                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> zlibbioc                /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> zoo                     /home/konrad/R/x86_64-pc-linux-gnu-library/4.2
#> base                                                /usr/lib/R/library
#> boot                                                /usr/lib/R/library
#> class                                               /usr/lib/R/library
#> cluster                                             /usr/lib/R/library
#> codetools                                           /usr/lib/R/library
#> compiler                                            /usr/lib/R/library
#> datasets                                            /usr/lib/R/library
#> foreign                                             /usr/lib/R/library
#> graphics                                            /usr/lib/R/library
#> grDevices                                           /usr/lib/R/library
#> grid                                                /usr/lib/R/library
#> KernSmooth                                          /usr/lib/R/library
#> lattice                                             /usr/lib/R/library
#> MASS                                                /usr/lib/R/library
#> Matrix                                              /usr/lib/R/library
#> methods                                             /usr/lib/R/library
#> mgcv                                                /usr/lib/R/library
#> nlme                                                /usr/lib/R/library
#> nnet                                                /usr/lib/R/library
#> parallel                                            /usr/lib/R/library
#> rpart                                               /usr/lib/R/library
#> spatial                                             /usr/lib/R/library
#> splines                                             /usr/lib/R/library
#> stats                                               /usr/lib/R/library
#> stats4                                              /usr/lib/R/library
#> survival                                            /usr/lib/R/library
#> tcltk                                               /usr/lib/R/library
#> tools                                               /usr/lib/R/library
#> utils                                               /usr/lib/R/library
#>                            Version    Priority
#> abind                        1.4-5        <NA>
#> affy                        1.74.0        <NA>
#> affyio                      1.66.0        <NA>
#> annotate                    1.74.0        <NA>
#> AnnotationDbi               1.58.0        <NA>
#> ape                          5.6-2        <NA>
#> aplot                        0.1.4        <NA>
#> arm                         1.12-2        <NA>
#> arules                       1.7-3        <NA>
#> askpass                        1.1        <NA>
#> assertthat                   0.2.1        <NA>
#> autokeras                   1.0.12        <NA>
#> backports                    1.4.1        <NA>
#> base64enc                    0.1-3        <NA>
#> BBmisc                        1.12        <NA>
#> BH                        1.78.0-0        <NA>
#> Biobase                     2.56.0        <NA>
#> BiocCheck                   1.32.0        <NA>
#> BiocFileCache                2.4.0        <NA>
#> BiocGenerics                0.42.0        <NA>
#> BiocManager                1.30.18        <NA>
#> Biocomb                        0.4        <NA>
#> BiocParallel                1.30.2        <NA>
#> BiocStyle                   2.24.0        <NA>
#> BiocVersion                 3.15.2        <NA>
#> biocViews                   1.64.0        <NA>
#> biomaRt                     2.52.0        <NA>
#> Biostrings                  2.64.0        <NA>
#> bit                          4.0.4        <NA>
#> bit64                        4.0.5        <NA>
#> bitops                       1.0-7        <NA>
#> blob                         1.2.3        <NA>
#> bookdown                      0.26        <NA>
#> Boruta                       7.0.0        <NA>
#> bounceR                        0.1        <NA>
#> brew                         1.0-7        <NA>
#> brio                         1.1.3        <NA>
#> broom                        0.8.0        <NA>
#> broom.helpers                1.7.0        <NA>
#> bslib                        0.3.1        <NA>
#> C50                          0.1.6        <NA>
#> cachem                       1.0.6        <NA>
#> calibrate                    1.7.7        <NA>
#> callr                        3.7.0        <NA>
#> car                         3.0-13        <NA>
#> carData                      3.0-5        <NA>
#> caret                       6.0-92        <NA>
#> caTools                     1.18.2        <NA>
#> cellranger                   1.1.0        <NA>
#> checkmate                    2.1.0        <NA>
#> circlize                    0.4.15        <NA>
#> classInt                     0.4-3        <NA>
#> cli                          3.3.0        <NA>
#> clipr                        0.8.0        <NA>
#> clue                        0.3-61        <NA>
#> clusterProfiler              4.4.1        <NA>
#> coda                        0.19-4        <NA>
#> coin                         1.4-2        <NA>
#> colorspace                   2.0-3        <NA>
#> combinat                     0.0-8        <NA>
#> commonmark                   1.8.0        <NA>
#> ComplexHeatmap              2.12.0        <NA>
#> config                       0.3.1        <NA>
#> corrplot                      0.92        <NA>
#> cowplot                      1.1.1        <NA>
#> cpp11                        0.4.2        <NA>
#> crayon                       1.5.1        <NA>
#> credentials                  1.3.2        <NA>
#> crosstalk                    1.2.0        <NA>
#> cubature                   2.0.4.4        <NA>
#> Cubist                       0.4.0        <NA>
#> curl                         4.3.2        <NA>
#> cutpointr                    1.1.2        <NA>
#> data.table                  1.14.2        <NA>
#> DBI                          1.1.2        <NA>
#> dbplyr                       2.1.1        <NA>
#> dbscan                      1.1-10        <NA>
#> deepnet                        0.2        <NA>
#> DelayedArray                0.22.0        <NA>
#> DEoptimR                    1.0-11        <NA>
#> Deriv                        4.1.3        <NA>
#> desc                         1.4.1        <NA>
#> DESeq2                      1.36.0        <NA>
#> devtools                     2.4.3        <NA>
#> DiceKriging                  1.6.0        <NA>
#> diffobj                      0.3.5        <NA>
#> digest                      0.6.29        <NA>
#> DMwR                         0.4.1        <NA>
#> DO.db                          2.9        <NA>
#> doParallel                  1.0.17        <NA>
#> DOSE                        3.22.0        <NA>
#> downlit                      0.4.0        <NA>
#> downloader                     0.4        <NA>
#> dplyr                        1.0.9        <NA>
#> DT                            0.23        <NA>
#> dtplyr                       1.2.1        <NA>
#> e1071                        1.7-9        <NA>
#> edgeR                       3.38.1        <NA>
#> ellipsis                     0.3.2        <NA>
#> enrichplot                  1.16.1        <NA>
#> entropy                      1.3.1        <NA>
#> epiDisplay                 3.5.0.2        <NA>
#> evaluate                      0.15        <NA>
#> exactRankTests              0.8-35        <NA>
#> fansi                        1.0.3        <NA>
#> farver                       2.1.0        <NA>
#> fastmap                      1.1.0        <NA>
#> fastmatch                    1.1-3        <NA>
#> feseR                        0.2.0        <NA>
#> fgsea                       1.22.0        <NA>
#> filelock                     1.0.2        <NA>
#> fontawesome                  0.2.2        <NA>
#> forcats                      0.5.1        <NA>
#> foreach                      1.5.2        <NA>
#> formatR                       1.12        <NA>
#> Formula                      1.2-4        <NA>
#> fs                           1.5.2        <NA>
#> FSelector                     0.33        <NA>
#> funModeling                  1.9.4        <NA>
#> furrr                        0.3.0        <NA>
#> futile.logger                1.4.3        <NA>
#> futile.options               1.0.1        <NA>
#> future                      1.26.1        <NA>
#> future.apply                 1.9.0        <NA>
#> gargle                       1.2.0        <NA>
#> gdata                     2.18.0.1        <NA>
#> GDCRNATools                 1.16.2        <NA>
#> genefilter                  1.78.0        <NA>
#> geneplotter                 1.74.0        <NA>
#> generics                     0.1.2        <NA>
#> GenomeInfoDb                1.32.2        <NA>
#> GenomeInfoDbData             1.2.8        <NA>
#> GenomicDataCommons          1.20.1        <NA>
#> GenomicRanges               1.48.0        <NA>
#> gert                         1.6.0        <NA>
#> GetoptLong                   1.0.5        <NA>
#> ggbiplot                      0.55        <NA>
#> ggforce                      0.3.3        <NA>
#> ggfun                        0.0.6        <NA>
#> ggplot2                      3.3.6        <NA>
#> ggplotify                    0.1.0        <NA>
#> ggpubr                       0.4.0        <NA>
#> ggraph                       2.0.5        <NA>
#> ggrepel                      0.9.1        <NA>
#> ggsci                          2.9        <NA>
#> ggsignif                     0.6.3        <NA>
#> ggtext                       0.1.1        <NA>
#> ggtree                       3.4.0        <NA>
#> gh                           1.3.0        <NA>
#> gitcreds                     0.1.1        <NA>
#> gld                          2.6.4        <NA>
#> glmnet                       4.1-4        <NA>
#> GlobalOptions                0.1.2        <NA>
#> globals                     0.15.0        <NA>
#> glue                         1.6.2        <NA>
#> gmodels                   2.18.1.1        <NA>
#> GO.db                       3.15.0        <NA>
#> googledrive                  2.0.0        <NA>
#> googlesheets4                1.0.0        <NA>
#> GOSemSim                    2.22.0        <NA>
#> gower                        1.0.0        <NA>
#> gplots                       3.1.3        <NA>
#> graph                       1.74.0        <NA>
#> graphlayouts                 0.8.0        <NA>
#> gridExtra                      2.3        <NA>
#> gridGraphics                 0.5-1        <NA>
#> gridtext                     0.1.4        <NA>
#> gt                           0.6.0        <NA>
#> gtable                       0.3.0        <NA>
#> gtools                     3.9.2.1        <NA>
#> gtsummary                    1.6.0        <NA>
#> hardhat                      0.2.0        <NA>
#> hash                       2.2.6.2        <NA>
#> haven                        2.5.0        <NA>
#> here                         1.0.1        <NA>
#> highr                          0.9        <NA>
#> Hmisc                        4.7-0        <NA>
#> hms                          1.1.1        <NA>
#> htmlTable                    2.4.0        <NA>
#> htmltools                    0.5.2        <NA>
#> htmlwidgets                  1.5.4        <NA>
#> HTqPCR                      1.50.0        <NA>
#> httpuv                       1.6.5        <NA>
#> httr                         1.4.3        <NA>
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#> igraph                       1.3.1        <NA>
#> imputeMissings               0.0.3        <NA>
#> ini                          0.3.1        <NA>
#> inum                         1.0-4        <NA>
#> ipred                       0.9-12        <NA>
#> IRanges                     2.30.0        <NA>
#> isoband                      0.2.5        <NA>
#> iterators                   1.0.14        <NA>
#> jpeg                         0.1-9        <NA>
#> jquerylib                    0.1.4        <NA>
#> jsonlite                     1.8.0        <NA>
#> kableExtra                   1.3.4        <NA>
#> KEGGgraph                   1.56.0        <NA>
#> KEGGREST                    1.36.0        <NA>
#> keras                        2.9.0        <NA>
#> kernlab                     0.9-30        <NA>
#> klaR                         1.7-0        <NA>
#> km.ci                        0.5-6        <NA>
#> KMsurv                       0.1-5        <NA>
#> knitr                         1.39        <NA>
#> labeling                     0.4.2        <NA>
#> labelled                     2.9.1        <NA>
#> laeken                       0.5.2        <NA>
#> lambda.r                     1.2.4        <NA>
#> later                        1.3.0        <NA>
#> latticeExtra                0.6-29        <NA>
#> lava                        1.6.10        <NA>
#> lavaan                      0.6-11        <NA>
#> lazyeval                     0.2.2        <NA>
#> lhs                          1.1.5        <NA>
#> libcoin                      1.0-9        <NA>
#> lifecycle                    1.0.1        <NA>
#> limma                       3.52.1        <NA>
#> listenv                      0.8.0        <NA>
#> lme4                        1.1-29        <NA>
#> lmom                           2.9        <NA>
#> lmtest                      0.9-40        <NA>
#> lobstr                       1.1.1        <NA>
#> locfit                     1.5-9.5        <NA>
#> lubridate                    1.8.0        <NA>
#> magick                       2.7.3        <NA>
#> magrittr                     2.0.3        <NA>
#> maptools                     1.1-4        <NA>
#> markdown                       1.1        <NA>
#> MatchIt                      4.4.0        <NA>
#> MatrixGenerics               1.8.0        <NA>
#> MatrixModels                 0.5-0        <NA>
#> matrixStats                 0.62.0        <NA>
#> maxstat                     0.7-25        <NA>
#> mboost                       2.9-7        <NA>
#> memoise                      2.0.1        <NA>
#> mice                        3.14.0        <NA>
#> mime                          0.12        <NA>
#> miniUI                     0.1.1.1        <NA>
#> minqa                        1.2.4        <NA>
#> mitools                        2.4        <NA>
#> mlbench                      2.1-3        <NA>
#> mlr                         2.19.0        <NA>
#> mnormt                       2.0.2        <NA>
#> ModelMetrics               1.2.2.2        <NA>
#> modelr                       0.1.8        <NA>
#> modeltools                  0.2-23        <NA>
#> moments                     0.14.1        <NA>
#> mRMRe                        2.1.2        <NA>
#> multcomp                    1.4-19        <NA>
#> munsell                      0.5.0        <NA>
#> mvtnorm                      1.1-3        <NA>
#> My.stepwise                  0.1.0        <NA>
#> naniar                       0.6.1        <NA>
#> networkD3                      0.4        <NA>
#> nloptr                       2.0.3        <NA>
#> nnls                           1.4        <NA>
#> nondetects                  2.26.0        <NA>
#> norm                      1.0-10.0        <NA>
#> np                         0.60-11        <NA>
#> numDeriv                2016.8-1.1        <NA>
#> OmicSelector                 1.0.0        <NA>
#> openssl                      2.0.2        <NA>
#> org.Hs.eg.db                3.15.0        <NA>
#> PairedData                   1.1.1        <NA>
#> pamr                        1.56.1        <NA>
#> pander                       0.6.5        <NA>
#> parallelly                  1.31.1        <NA>
#> parallelMap                  1.5.1        <NA>
#> ParamHelpers                  1.14        <NA>
#> ParBayesianOptimization      1.2.4        <NA>
#> parsetools                   0.1.3        <NA>
#> party                       1.3-10        <NA>
#> partykit                    1.2-15        <NA>
#> patchwork                    1.1.1        <NA>
#> pathview                    1.36.0        <NA>
#> pbivnorm                     0.6.0        <NA>
#> pbkrtest                     0.5.1        <NA>
#> pillar                       1.7.0        <NA>
#> pkgbuild                     1.3.1        <NA>
#> pkgcond                      0.1.1        <NA>
#> pkgconfig                    2.0.3        <NA>
#> pkgdown                      2.0.3        <NA>
#> pkgload                      1.2.4        <NA>
#> plogr                        0.2.0        <NA>
#> plotly                      4.10.0        <NA>
#> plyr                         1.8.7        <NA>
#> png                          0.1-7        <NA>
#> polspline                   1.1.20        <NA>
#> polyclip                    1.10-0        <NA>
#> polynom                      1.4-1        <NA>
#> postlogic                  0.1.0.1        <NA>
#> praise                       1.0.0        <NA>
#> preprocessCore              1.58.0        <NA>
#> prettyunits                  1.1.1        <NA>
#> pROC                        1.18.0        <NA>
#> processx                     3.5.3        <NA>
#> prodlim                 2019.11.13        <NA>
#> profileR                     0.3-5        <NA>
#> progress                     1.2.2        <NA>
#> progressr                   0.10.0        <NA>
#> promises                   1.2.0.1        <NA>
#> proxy                       0.4-26        <NA>
#> pryr                         0.1.5        <NA>
#> ps                           1.7.0        <NA>
#> psych                        2.2.5        <NA>
#> purrr                        0.3.4        <NA>
#> purrrogress                  0.1.1        <NA>
#> quadprog                     1.5-8        <NA>
#> quantmod                    0.4.20        <NA>
#> quantreg                      5.93        <NA>
#> questionr                    0.7.7        <NA>
#> qvalue                      2.28.0        <NA>
#> R.cache                     0.15.0        <NA>
#> R.methodsS3                  1.8.1        <NA>
#> R.oo                        1.24.0        <NA>
#> R.utils                     2.11.0        <NA>
#> R6                           2.5.1        <NA>
#> ragg                         1.2.2        <NA>
#> randomForest               4.7-1.1        <NA>
#> ranger                      0.13.1        <NA>
#> RANN                         2.6.1        <NA>
#> rappdirs                     0.3.3        <NA>
#> rapportools                    1.1        <NA>
#> RBGL                        1.72.0        <NA>
#> rcmdcheck                    1.4.0        <NA>
#> RColorBrewer                 1.1-3        <NA>
#> Rcpp                       1.0.8.3        <NA>
#> RcppArmadillo           0.11.1.1.0        <NA>
#> RcppEigen                0.3.3.9.2        <NA>
#> RcppProgress                 0.4.2        <NA>
#> RcppTOML                     0.1.7        <NA>
#> RCurl                     1.98-1.6        <NA>
#> readr                        2.1.2        <NA>
#> readxl                       1.4.0        <NA>
#> recipes                      0.2.0        <NA>
#> rematch                      1.0.1        <NA>
#> rematch2                     2.1.2        <NA>
#> remotes                      2.4.2        <NA>
#> reprex                       2.0.1        <NA>
#> resample                       0.4        <NA>
#> reshape                      0.8.9        <NA>
#> reshape2                     1.4.4        <NA>
#> reticulate                    1.25        <NA>
#> rgl                      0.108.3.2        <NA>
#> Rgraphviz                   2.40.0        <NA>
#> rhandsontable                0.3.8        <NA>
#> rJava                        1.0-6        <NA>
#> rjson                       0.2.21        <NA>
#> rlang                        1.0.2        <NA>
#> rmarkdown                     2.14        <NA>
#> rms                          6.3-0        <NA>
#> robustbase                  0.95-0        <NA>
#> ROCR                        1.0-11        <NA>
#> ROSE                         0.0-4        <NA>
#> roxygen2                     7.2.0        <NA>
#> rprojroot                    2.0.3        <NA>
#> RSNNS                       0.4-14        <NA>
#> rsq                            2.5        <NA>
#> RSQLite                     2.2.14        <NA>
#> rstatix                      0.7.0        <NA>
#> rstudioapi                    0.13        <NA>
#> RUnit                       0.4.32        <NA>
#> rversions                    2.1.1        <NA>
#> rvest                        1.0.2        <NA>
#> RWeka                       0.4-44        <NA>
#> RWekajars                  3.9.3-2        <NA>
#> S4Vectors                   0.34.0        <NA>
#> sandwich                     3.0-1        <NA>
#> sass                         0.4.1        <NA>
#> scales                       1.2.0        <NA>
#> scatterpie                   0.1.7        <NA>
#> selectr                      0.4-2        <NA>
#> sessioninfo                  1.2.2        <NA>
#> shadowtext                   0.1.2        <NA>
#> shape                        1.4.6        <NA>
#> shiny                        1.7.1        <NA>
#> shinyfullscreen              1.1.0        <NA>
#> shinyjqui                    0.4.1        <NA>
#> shinyjs                      2.1.0        <NA>
#> snow                         0.4-4        <NA>
#> sourcetools                  0.1.7        <NA>
#> sp                           1.4-7        <NA>
#> SparseM                       1.81        <NA>
#> spFSR                        1.0.0        <NA>
#> SQUAREM                     2021.1        <NA>
#> stabs                        0.6-4        <NA>
#> stargazer                    5.2.3        <NA>
#> stringdist                   0.9.8        <NA>
#> stringi                      1.7.6        <NA>
#> stringr                      1.4.0        <NA>
#> strucchange                  1.5-2        <NA>
#> styler                       1.7.0        <NA>
#> SummarizedExperiment        1.26.1        <NA>
#> summarytools                 1.0.1        <NA>
#> survey                       4.1-1        <NA>
#> survminer                    0.4.9        <NA>
#> survMisc                     0.5.6        <NA>
#> sva                         3.44.0        <NA>
#> svglite                      2.1.0        <NA>
#> sys                            3.4        <NA>
#> systemfonts                  1.0.4        <NA>
#> tableone                    0.13.2        <NA>
#> TCGAbiolinks                2.24.1        <NA>
#> TCGAbiolinksGUI.data        1.16.0        <NA>
#> tensorflow                   2.9.0        <NA>
#> testextra               0.1.0.9000        <NA>
#> testthat                     3.1.4        <NA>
#> textshaping                  0.3.6        <NA>
#> tfautograph                  0.3.2        <NA>
#> tfruns                       1.5.0        <NA>
#> TH.data                      1.1-1        <NA>
#> tibble                       3.1.7        <NA>
#> tictoc                       1.0.1        <NA>
#> tidygraph                    1.2.1        <NA>
#> tidyr                        1.2.0        <NA>
#> tidyselect                   1.1.2        <NA>
#> tidytemplate                 1.0.0        <NA>
#> tidytree                     0.3.9        <NA>
#> tidyverse                    1.3.1        <NA>
#> timeDate                  3043.102        <NA>
#> tinytex                       0.39        <NA>
#> tmvnsim                      1.0-2        <NA>
#> treeio                      1.20.0        <NA>
#> TTR                         0.24.3        <NA>
#> tweenr                       1.0.2        <NA>
#> tzdb                         0.3.0        <NA>
#> UpSetR                       1.4.0        <NA>
#> usethis                      2.1.6        <NA>
#> utf8                         1.2.2        <NA>
#> uuid                         1.1-0        <NA>
#> varSelRF                     0.7-8        <NA>
#> vcd                          1.4-9        <NA>
#> vctrs                        0.4.1        <NA>
#> VennDiagram                  1.7.3        <NA>
#> VIM                          6.1.1        <NA>
#> viridis                      0.6.2        <NA>
#> viridisLite                  0.4.0        <NA>
#> visdat                       0.5.3        <NA>
#> vroom                        1.5.7        <NA>
#> waiter                  0.2.5.9000        <NA>
#> waldo                        0.4.0        <NA>
#> webshot                      0.5.3        <NA>
#> whisker                        0.4        <NA>
#> withr                        2.5.0        <NA>
#> xfun                          0.31        <NA>
#> xgboost                    1.6.0.1        <NA>
#> xlsx                         0.6.5        <NA>
#> xlsxjars                     0.6.1        <NA>
#> XML                       3.99-0.9        <NA>
#> xml2                         1.3.3        <NA>
#> xopen                        1.0.0        <NA>
#> xtable                       1.8-4        <NA>
#> xts                         0.12.1        <NA>
#> XVector                     0.36.0        <NA>
#> yaml                         2.3.5        <NA>
#> yulab.utils                  0.0.4        <NA>
#> zeallot                      0.1.0        <NA>
#> zip                          2.2.0        <NA>
#> zlibbioc                    1.42.0        <NA>
#> zoo                         1.8-10        <NA>
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#> class                       7.3-20 recommended
#> cluster                      2.1.3 recommended
#> codetools                   0.2-18 recommended
#> compiler                     4.2.0        base
#> datasets                     4.2.0        base
#> foreign                     0.8-82 recommended
#> graphics                     4.2.0        base
#> grDevices                    4.2.0        base
#> grid                         4.2.0        base
#> KernSmooth                 2.23-20 recommended
#> lattice                    0.20-45 recommended
#> MASS                        7.3-57 recommended
#> Matrix                       1.4-1 recommended
#> methods                      4.2.0        base
#> mgcv                        1.8-40 recommended
#> nlme                       3.1-157 recommended
#> nnet                        7.3-17 recommended
#> parallel                     4.2.0        base
#> rpart                       4.1.16 recommended
#> spatial                     7.3-11 recommended
#> splines                      4.2.0        base
#> stats                        4.2.0        base
#> stats4                       4.2.0        base
#> survival                    3.2-13 recommended
#> tcltk                        4.2.0        base
#> tools                        4.2.0        base
#> utils                        4.2.0        base
#>                                                                                                                                                          Depends
#> abind                                                                                                                                               R (>= 1.5.0)
#> affy                                                                                                  R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5)
#> affyio                                                                                                                                              R (>= 2.6.0)
#> annotate                                                                                                             R (>= 2.10), AnnotationDbi (>= 1.27.5), XML
#> AnnotationDbi                                                      R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>=\n0.29.2), Biobase (>= 1.17.0), IRanges
#> ape                                                                                                                                                 R (>= 3.2.0)
#> aplot                                                                                                                                                       <NA>
#> arm                                                                                                    R (>= 3.1.0), MASS, Matrix (>= 1.0), stats, lme4 (>= 1.0)
#> arules                                                                                                                           R (>= 4.0.0), Matrix (>= 1.2-0)
#> askpass                                                                                                                                                     <NA>
#> assertthat                                                                                                                                                  <NA>
#> autokeras                                                                                                                                             R (>= 3.1)
#> backports                                                                                                                                           R (>= 3.0.0)
#> base64enc                                                                                                                                           R (>= 2.9.0)
#> BBmisc                                                                                                                                                      <NA>
#> BH                                                                                                                                                          <NA>
#> Biobase                                                                                                             R (>= 2.10), BiocGenerics (>= 0.27.1), utils
#> BiocCheck                                                                                                                                           R (>= 4.2.0)
#> BiocFileCache                                                                                                                    R (>= 3.4.0), dbplyr (>= 1.0.0)
#> BiocGenerics                                                                                                       R (>= 4.0.0), methods, utils, graphics, stats
#> BiocManager                                                                                                                                                 <NA>
#> Biocomb                                                                                                                    R (>= 2.13.0),gtools,Rcpp (>= 0.12.1)
#> BiocParallel                                                                                                                               methods, R (>= 3.5.0)
#> BiocStyle                                                                                                                                                   <NA>
#> BiocVersion                                                                                                                                         R (>= 4.2.0)
#> biocViews                                                                                                                                           R (>= 3.6.0)
#> biomaRt                                                                                                                                                  methods
#> Biostrings                     R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>=\n0.27.12), IRanges (>= 2.23.9), XVector (>= 0.29.2),\nGenomeInfoDb
#> bit                                                                                                                                                 R (>= 2.9.2)
#> bit64                                                                                                        R (>= 3.0.1), bit (>= 4.0.0), utils, methods, stats
#> bitops                                                                                                                                                      <NA>
#> blob                                                                                                                                                        <NA>
#> bookdown                                                                                                                                                    <NA>
#> Boruta                                                                                                                                                      <NA>
#> bounceR                                                                                                                                             R (>= 3.4.3)
#> brew                                                                                                                                                        <NA>
#> brio                                                                                                                                                        <NA>
#> broom                                                                                                                                                 R (>= 3.1)
#> broom.helpers                                                                                                                                         R (>= 3.4)
#> bslib                                                                                                                                                R (>= 2.10)
#> C50                                                                                                                                                R (>= 2.10.0)
#> cachem                                                                                                                                                      <NA>
#> calibrate                                                                                                                                     R (>= 3.5.0), MASS
#> callr                                                                                                                                                       <NA>
#> car                                                                                                                             R (>= 3.5.0), carData (>= 3.0-0)
#> carData                                                                                                                                             R (>= 3.5.0)
#> caret                                                                                                                   ggplot2, lattice (>= 0.20), R (>= 3.2.0)
#> caTools                                                                                                                                             R (>= 3.6.0)
#> cellranger                                                                                                                                          R (>= 3.0.0)
#> checkmate                                                                                                                                           R (>= 3.0.0)
#> circlize                                                                                                                                  R (>= 3.0.0), graphics
#> classInt                                                                                                                                              R (>= 2.2)
#> cli                                                                                                                                                   R (>= 3.4)
#> clipr                                                                                                                                                       <NA>
#> clue                                                                                                                                                R (>= 3.2.0)
#> clusterProfiler                                                                                                                                     R (>= 3.5.0)
#> coda                                                                                                                                               R (>= 2.14.0)
#> coin                                                                                                                                      R (>= 3.6.0), survival
#> colorspace                                                                                                                                 R (>= 3.0.0), methods
#> combinat                                                                                                                                                    <NA>
#> commonmark                                                                                                                                                  <NA>
#> ComplexHeatmap                                                                                           R (>= 3.5.0), methods, grid, graphics, stats, grDevices
#> config                                                                                                                                                      <NA>
#> corrplot                                                                                                                                                    <NA>
#> cowplot                                                                                                                                             R (>= 3.5.0)
#> cpp11                                                                                                                                                       <NA>
#> crayon                                                                                                                                                      <NA>
#> credentials                                                                                                                                                 <NA>
#> crosstalk                                                                                                                                                   <NA>
#> cubature                                                                                                                                                    <NA>
#> Cubist                                                                                                                                                   lattice
#> curl                                                                                                                                                R (>= 3.0.0)
#> cutpointr                                                                                                                                           R (>= 3.5.0)
#> data.table                                                                                                                                          R (>= 3.1.0)
#> DBI                                                                                                                                        methods, R (>= 3.0.0)
#> dbplyr                                                                                                                                                R (>= 3.1)
#> dbscan                                                                                                                                                      <NA>
#> deepnet                                                                                                                                                     <NA>
#> DelayedArray            R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>=\n0.37.0), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.27.2),\nIRanges (>= 2.17.3)
#> DEoptimR                                                                                                                                                    <NA>
#> Deriv                                                                                                                                                       <NA>
#> desc                                                                                                                                                  R (>= 3.4)
#> DESeq2                                                                          S4Vectors (>= 0.23.18), IRanges, GenomicRanges,\nSummarizedExperiment (>= 1.1.6)
#> devtools                                                                                                                        R (>= 3.0.2), usethis (>= 2.0.1)
#> DiceKriging                                                                                                                                              methods
#> diffobj                                                                                                                                             R (>= 3.1.0)
#> digest                                                                                                                                              R (>= 3.3.0)
#> DMwR                                                                                       R(>= 2.10), methods, graphics, lattice (>= 0.18-3), grid (>=\n2.10.1)
#> DO.db                                                                                                            R (>= 2.7.0), methods, AnnotationDbi (>= 1.9.7)
#> doParallel                                                                             R (>= 2.14.0), foreach (>= 1.2.0), iterators (>= 1.0.0),\nparallel, utils
#> DOSE                                                                                                                                                R (>= 3.5.0)
#> downlit                                                                                                                                             R (>= 3.4.0)
#> downloader                                                                                                                                                  <NA>
#> dplyr                                                                                                                                               R (>= 3.4.0)
#> DT                                                                                                                                                          <NA>
#> dtplyr                                                                                                                                                R (>= 3.3)
#> e1071                                                                                                                                                       <NA>
#> edgeR                                                                                                                            R (>= 3.6.0), limma (>= 3.41.5)
#> ellipsis                                                                                                                                              R (>= 3.2)
#> enrichplot                                                                                                                                          R (>= 3.5.0)
#> entropy                                                                                                                                             R (>= 3.0.2)
#> epiDisplay                                                                                                           R (>= 2.6.2), foreign, survival, MASS, nnet
#> evaluate                                                                                                                                            R (>= 3.0.2)
#> exactRankTests                                                                                                                        R (>= 2.4.0), stats, utils
#> fansi                                                                                                                                               R (>= 3.1.0)
#> farver                                                                                                                                                      <NA>
#> fastmap                                                                                                                                                     <NA>
#> fastmatch                                                                                                                                           R (>= 2.3.0)
#> feseR                                                                                                                                                R (>= 2.10)
#> fgsea                                                                                                                                                 R (>= 3.3)
#> filelock                                                                                                                                                    <NA>
#> fontawesome                                                                                                                                         R (>= 3.3.0)
#> forcats                                                                                                                                               R (>= 3.2)
#> foreach                                                                                                                                             R (>= 2.5.0)
#> formatR                                                                                                                                             R (>= 3.2.3)
#> Formula                                                                                                                                      R (>= 2.0.0), stats
#> fs                                                                                                                                                    R (>= 3.1)
#> FSelector                                                                                                                                                   <NA>
#> funModeling                                                                                                                      R (>= 3.4.0), Hmisc (>= 3.17.1)
#> furrr                                                                                                                           future (>= 1.25.0), R (>= 3.4.0)
#> futile.logger                                                                                                                                       R (>= 3.0.0)
#> futile.options                                                                                                                                      R (>= 2.8.0)
#> future                                                                                                                                                      <NA>
#> future.apply                                                                                                                    R (>= 3.2.0), future (>= 1.22.1)
#> gargle                                                                                                                                                R (>= 3.3)
#> gdata                                                                                                                                               R (>= 2.3.0)
#> GDCRNATools                                                                                                                                         R (>= 3.5.0)
#> genefilter                                                                                                                                                  <NA>
#> geneplotter                                                                                       R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate
#> generics                                                                                                                                              R (>= 3.2)
#> GenomeInfoDb                                                      R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>=\n0.25.12), IRanges (>= 2.13.12)
#> GenomeInfoDbData                                                                                                                                    R (>= 3.5.0)
#> GenomicDataCommons                                                                                                                        R (>= 3.4.0), magrittr
#> GenomicRanges                   R (>= 4.0.0), methods, stats4, BiocGenerics (>= 0.37.0),\nS4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>=\n1.15.2)
#> gert                                                                                                                                                        <NA>
#> GetoptLong                                                                                                                                          R (>= 3.3.0)
#> ggbiplot                                                                                                                             ggplot2, plyr, scales, grid
#> ggforce                                                                                                                         ggplot2 (>= 3.0.0), R (>= 3.3.0)
#> ggfun                                                                                                                                                       <NA>
#> ggplot2                                                                                                                                               R (>= 3.3)
#> ggplotify                                                                                                                                           R (>= 3.4.0)
#> ggpubr                                                                                                                                     R (>= 3.1.0), ggplot2
#> ggraph                                                                                                                           R (>= 2.10), ggplot2 (>= 3.0.0)
#> ggrepel                                                                                                                         R (>= 3.0.0), ggplot2 (>= 2.2.0)
#> ggsci                                                                                                                                               R (>= 3.0.2)
#> ggsignif                                                                                                                                                    <NA>
#> ggtext                                                                                                                                                R (>= 3.5)
#> ggtree                                                                                                                                              R (>= 3.5.0)
#> gh                                                                                                                                                          <NA>
#> gitcreds                                                                                                                                                    <NA>
#> gld                                                                                                                                                         <NA>
#> glmnet                                                                                                                           R (>= 3.6.0), Matrix (>= 1.0-6)
#> GlobalOptions                                                                                                                              R (>= 3.3.0), methods
#> globals                                                                                                                                             R (>= 3.1.2)
#> glue                                                                                                                                                  R (>= 3.4)
#> gmodels                                                                                                                                             R (>= 1.9.0)
#> GO.db                                                                                                           R (>= 2.7.0), methods, AnnotationDbi (>= 1.57.1)
#> googledrive                                                                                                                                           R (>= 3.3)
#> googlesheets4                                                                                                                                         R (>= 3.3)
#> GOSemSim                                                                                                                                            R (>= 3.5.0)
#> gower                                                                                                                                                       <NA>
#> gplots                                                                                                                                                R (>= 3.0)
#> graph                                                                                                            R (>= 2.10), methods, BiocGenerics (>= 0.13.11)
#> graphlayouts                                                                                                                                        R (>= 3.2.0)
#> gridExtra                                                                                                                                                   <NA>
#> gridGraphics                                                                                                                                      grid, graphics
#> gridtext                                                                                                                                              R (>= 3.5)
#> gt                                                                                                                                                  R (>= 3.2.0)
#> gtable                                                                                                                                                R (>= 3.0)
#> gtools                                                                                                                        R (>= 2.10), methods, stats, utils
#> gtsummary                                                                                                                                             R (>= 3.4)
#> hardhat                                                                                                                                              R (>= 2.10)
#> hash                                                                                                                               R (>= 2.12.0), methods, utils
#> haven                                                                                                                                                 R (>= 3.4)
#> here                                                                                                                                                        <NA>
#> highr                                                                                                                                               R (>= 3.2.3)
#> Hmisc                                                                                                    lattice, survival (>= 3.1-6), Formula, ggplot2 (>= 2.2)
#> hms                                                                                                                                                         <NA>
#> htmlTable                                                                                                                                                   <NA>
#> htmltools                                                                                                                                          R (>= 2.14.1)
#> htmlwidgets                                                                                                                                                 <NA>
#> HTqPCR                                                                                                                              Biobase, RColorBrewer, limma
#> httpuv                                                                                                                                             R (>= 2.15.1)
#> httr                                                                                                                                                  R (>= 3.2)
#> ids                                                                                                                                                         <NA>
#> igraph                                                                                                                                                   methods
#> imputeMissings                                                                                                                                              <NA>
#> ini                                                                                                                                                         <NA>
#> inum                                                                                                                                                R (>= 3.3.0)
#> ipred                                                                                                                                                R (>= 2.10)
#> IRanges                                                                    R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.39.2),\nS4Vectors (>= 0.33.3)
#> isoband                                                                                                                                                     <NA>
#> iterators                                                                                                                                    R (>= 2.5.0), utils
#> jpeg                                                                                                                                                R (>= 2.9.0)
#> jquerylib                                                                                                                                                   <NA>
#> jsonlite                                                                                                                                                 methods
#> kableExtra                                                                                                                                          R (>= 3.1.0)
#> KEGGgraph                                                                                                                                           R (>= 3.5.0)
#> KEGGREST                                                                                                                                            R (>= 3.5.0)
#> keras                                                                                                                                                 R (>= 3.4)
#> kernlab                                                                                                                                              R (>= 2.10)
#> klaR                                                                                                                                         R (>= 2.10.0), MASS
#> km.ci                                                                                                                                               R (>= 3.5.0)
#> KMsurv                                                                                                                                                      <NA>
#> knitr                                                                                                                                               R (>= 3.3.0)
#> labeling                                                                                                                                                    <NA>
#> labelled                                                                                                                                              R (>= 3.0)
#> laeken                                                                                                                                              R (>= 3.2.0)
#> lambda.r                                                                                                                                            R (>= 3.0.0)
#> later                                                                                                                                                       <NA>
#> latticeExtra                                                                                                                               R (>= 3.6.0), lattice
#> lava                                                                                                                                                  R (>= 3.0)
#> lavaan                                                                                                                                                 R(>= 3.4)
#> lazyeval                                                                                                                                            R (>= 3.1.0)
#> lhs                                                                                                                                                 R (>= 3.4.0)
#> libcoin                                                                                                                                             R (>= 3.4.0)
#> lifecycle                                                                                                                                             R (>= 3.3)
#> limma                                                                                                                                               R (>= 3.6.0)
#> listenv                                                                                                                                             R (>= 3.1.2)
#> lme4                                                                                                             R (>= 3.2.0), Matrix (>= 1.2-1), methods, stats
#> lmom                                                                                                                                                R (>= 3.0.0)
#> lmtest                                                                                                                                  R (>= 3.0.0), stats, zoo
#> lobstr                                                                                                                                                R (>= 3.2)
#> locfit                                                                                                                                              R (>= 4.1.0)
#> lubridate                                                                                                                                    methods, R (>= 3.2)
#> magick                                                                                                                                                      <NA>
#> magrittr                                                                                                                                            R (>= 3.4.0)
#> maptools                                                                                                                             R (>= 2.10), sp (>= 1.0-11)
#> markdown                                                                                                                                           R (>= 2.11.1)
#> MatchIt                                                                                                                                             R (>= 3.1.0)
#> MatrixGenerics                                                                                                                           matrixStats (>= 0.60.1)
#> MatrixModels                                                                                                                                        R (>= 3.0.1)
#> matrixStats                                                                                                                                        R (>= 2.12.0)
#> maxstat                                                                                                                                             R (>= 1.7.0)
#> mboost                                                                                                  R (>= 3.2.0), methods, stats, parallel, stabs (>= 0.5-0)
#> memoise                                                                                                                                                     <NA>
#> mice                                                                                                                                               R (>= 2.10.0)
#> mime                                                                                                                                                        <NA>
#> miniUI                                                                                                                                                      <NA>
#> minqa                                                                                                                                                       <NA>
#> mitools                                                                                                                                                     <NA>
#> mlbench                                                                                                                                              R (>= 2.10)
#> mlr                                                                                                                         ParamHelpers (>= 1.10), R (>= 3.0.2)
#> mnormt                                                                                                                                              R (>= 2.2.0)
#> ModelMetrics                                                                                                                                        R (>= 3.2.2)
#> modelr                                                                                                                                                R (>= 3.2)
#> modeltools                                                                                                                                         stats, stats4
#> moments                                                                                                                                                     <NA>
#> mRMRe                                                                                                                      R (>= 3.5), survival, igraph, methods
#> multcomp                                                                         stats, graphics, mvtnorm (>= 1.0-10), survival (>= 2.39-4),\nTH.data (>= 1.0-2)
#> munsell                                                                                                                                                     <NA>
#> mvtnorm                                                                                                                                              R(>= 3.5.0)
#> My.stepwise                                                                                                                                         R (>= 3.3.3)
#> naniar                                                                                                                                              R (>= 3.1.2)
#> networkD3                                                                                                                                           R (>= 3.0.0)
#> nloptr                                                                                                                                                      <NA>
#> nnls                                                                                                                                                        <NA>
#> nondetects                                                                                                                       R (>= 3.2), Biobase (>= 2.22.0)
#> norm                                                                                                                                                        <NA>
#> np                                                                                                                                                          <NA>
#> numDeriv                                                                                                                                           R (>= 2.11.1)
#> OmicSelector                                                                                                                                         R (>= 2.10)
#> openssl                                                                                                                                                     <NA>
#> org.Hs.eg.db                                                                                                    R (>= 2.7.0), methods, AnnotationDbi (>= 1.57.1)
#> PairedData                                                                                                     methods,graphics,MASS,gld,mvtnorm,lattice,ggplot2
#> pamr                                                                                                                              R (>= 2.10), cluster, survival
#> pander                                                                                                                                             R (>= 2.15.0)
#> parallelly                                                                                                                                                  <NA>
#> parallelMap                                                                                                                                         R (>= 3.0.0)
#> ParamHelpers                                                                                                                                                <NA>
#> ParBayesianOptimization                                                                                                                               R (>= 3.4)
#> parsetools                                                                                                                                                  <NA>
#> party                                                               R (>= 3.0.0), methods, grid, stats, mvtnorm (>= 1.0-2),\nmodeltools (>= 0.2-21), strucchange
#> partykit                                                                                               R (>= 3.5.0), graphics, grid, libcoin (>= 1.0-0), mvtnorm
#> patchwork                                                                                                                                                   <NA>
#> pathview                                                                                                                                            R (>= 3.5.0)
#> pbivnorm                                                                                                                                                    <NA>
#> pbkrtest                                                                                                                          R (>= 3.5.0), lme4 (>= 1.1.10)
#> pillar                                                                                                                                                      <NA>
#> pkgbuild                                                                                                                                              R (>= 3.1)
#> pkgcond                                                                                                                                              R(>= 3.5.0)
#> pkgconfig                                                                                                                                                   <NA>
#> pkgdown                                                                                                                                             R (>= 3.1.0)
#> pkgload                                                                                                                                                     <NA>
#> plogr                                                                                                                                                       <NA>
#> plotly                                                                                                                          R (>= 3.2.0), ggplot2 (>= 3.0.0)
#> plyr                                                                                                                                                R (>= 3.1.0)
#> png                                                                                                                                                 R (>= 2.9.0)
#> polspline                                                                                                                                                   <NA>
#> polyclip                                                                                                                                            R (>= 3.0.0)
#> polynom                                                                                                                                                     <NA>
#> postlogic                                                                                                                                                   <NA>
#> praise                                                                                                                                                      <NA>
#> preprocessCore                                                                                                                                              <NA>
#> prettyunits                                                                                                                                                 <NA>
#> pROC                                                                                                                                                 R (>= 2.14)
#> processx                                                                                                                                            R (>= 3.4.0)
#> prodlim                                                                                                                                             R (>= 2.9.0)
#> profileR                                                                                                    ggplot2, RColorBrewer, reshape, lavaan, R (>= 3.0.0)
#> progress                                                                                                                                                    <NA>
#> progressr                                                                                                                                           R (>= 3.5.0)
#> promises                                                                                                                                                    <NA>
#> proxy                                                                                                                                               R (>= 3.4.0)
#> pryr                                                                                                                                                R (>= 3.1.0)
#> ps                                                                                                                                                    R (>= 3.4)
#> psych                                                                                                                                                       <NA>
#> purrr                                                                                                                                                 R (>= 3.2)
#> purrrogress                                                                                                                                                 <NA>
#> quadprog                                                                                                                                            R (>= 3.1.0)
#> quantmod                                                                                                  R (>= 3.2.0), xts(>= 0.9-0), zoo, TTR(>= 0.2), methods
#> quantreg                                                                                                                              R (>= 3.5), stats, SparseM
#> questionr                                                                                                                                           R (>= 3.5.0)
#> qvalue                                                                                                                                                R(>= 2.10)
#> R.cache                                                                                                                                            R (>= 2.14.0)
#> R.methodsS3                                                                                                                                        R (>= 2.13.0)
#> R.oo                                                                                                                       R (>= 2.13.0), R.methodsS3 (>= 1.8.0)
#> R.utils                                                                                                                          R (>= 2.14.0), R.oo (>= 1.24.0)
#> R6                                                                                                                                                    R (>= 3.0)
#> ragg                                                                                                                                                        <NA>
#> randomForest                                                                                                                                 R (>= 4.1.0), stats
#> ranger                                                                                                                                                R (>= 3.1)
#> RANN                                                                                                                                                        <NA>
#> rappdirs                                                                                                                                              R (>= 3.2)
#> rapportools                                                                                                                                                 <NA>
#> RBGL                                                                                                                                              graph, methods
#> rcmdcheck                                                                                                                                                   <NA>
#> RColorBrewer                                                                                                                                        R (>= 2.0.0)
#> Rcpp                                                                                                                                                        <NA>
#> RcppArmadillo                                                                                                                                       R (>= 3.3.0)
#> RcppEigen                                                                                                                                                   <NA>
#> RcppProgress                                                                                                                                                <NA>
#> RcppTOML                                                                                                                                            R (>= 3.3.0)
#> RCurl                                                                                                                                      R (>= 3.4.0), methods
#> readr                                                                                                                                                 R (>= 3.1)
#> readxl                                                                                                                                                R (>= 3.4)
#> recipes                                                                                                                                        dplyr, R (>= 3.1)
#> rematch                                                                                                                                                     <NA>
#> rematch2                                                                                                                                                    <NA>
#> remotes                                                                                                                                             R (>= 3.0.0)
#> reprex                                                                                                                                                R (>= 3.3)
#> resample                                                                                                                           R (>= 3.1.0), graphics, stats
#> reshape                                                                                                                                             R (>= 2.6.1)
#> reshape2                                                                                                                                              R (>= 3.1)
#> reticulate                                                                                                                                            R (>= 3.0)
#> rgl                                                                                                                                                 R (>= 3.3.0)
#> Rgraphviz                                                                                                              R (>= 2.6.0), methods, utils, graph, grid
#> rhandsontable                                                                                                                                               <NA>
#> rJava                                                                                                                                      R (>= 3.6.0), methods
#> rjson                                                                                                                                               R (>= 4.0.0)
#> rlang                                                                                                                                               R (>= 3.4.0)
#> rmarkdown                                                                                                                                             R (>= 3.0)
#> rms                                                                    R (>= 3.5.0), Hmisc (>= 4.7-0), survival (>= 3.1-12), lattice,\nggplot2 (>= 2.2), SparseM
#> robustbase                                                                                                                                          R (>= 3.5.0)
#> ROCR                                                                                                                                                  R (>= 3.6)
#> ROSE                                                                                                                                                        <NA>
#> roxygen2                                                                                                                                              R (>= 3.3)
#> rprojroot                                                                                                                                           R (>= 3.0.0)
#> RSNNS                                                                                                                    R (>= 2.10.0), methods, Rcpp (>= 0.8.5)
#> rsq                                                                                                                                                         <NA>
#> RSQLite                                                                                                                                             R (>= 3.1.0)
#> rstatix                                                                                                                                             R (>= 3.3.0)
#> rstudioapi                                                                                                                                                  <NA>
#> RUnit                                                                                   R (>= 2.5.0), utils (>= 2.5.0), methods (>= 2.5.0), graphics\n(>= 2.5.0)
#> rversions                                                                                                                                                   <NA>
#> rvest                                                                                                                                                 R (>= 3.2)
#> RWeka                                                                                                                                               R (>= 2.6.0)
#> RWekajars                                                                                                                                                   <NA>
#> S4Vectors                                                                                 R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>=\n0.37.0)
#> sandwich                                                                                                                                            R (>= 3.0.0)
#> sass                                                                                                                                                        <NA>
#> scales                                                                                                                                                R (>= 3.2)
#> scatterpie                                                                                                                                 R (>= 3.4.0), ggplot2
#> selectr                                                                                                                                               R (>= 3.0)
#> sessioninfo                                                                                                                                          R (>= 2.10)
#> shadowtext                                                                                                                                          R (>= 3.4.0)
#> shape                                                                                                                                                R (>= 2.01)
#> shiny                                                                                                                                      R (>= 3.0.2), methods
#> shinyfullscreen                                                                                                                                             <NA>
#> shinyjqui                                                                                                                                           R (>= 3.2.0)
#> shinyjs                                                                                                                                             R (>= 3.1.0)
#> snow                                                                                                                                        R (>= 2.13.1), utils
#> sourcetools                                                                                                                                         R (>= 3.0.2)
#> sp                                                                                                                                         R (>= 3.0.0), methods
#> SparseM                                                                                                                                     R (>= 2.15), methods
#> spFSR                                                                                 mlr (>= 2.11), parallelMap (>= 1.3), parallel (>= 3.4.2),\ntictoc (>= 1.0)
#> SQUAREM                                                                                                                                               R (>= 3.0)
#> stabs                                                                                                                    R (>= 2.14.0), methods, stats, parallel
#> stargazer                                                                                                                                                   <NA>
#> stringdist                                                                                                                                         R (>= 2.15.3)
#> stringi                                                                                                                                               R (>= 3.1)
#> stringr                                                                                                                                               R (>= 3.1)
#> strucchange                                                                                                                         R (>= 2.10.0), zoo, sandwich
#> styler                                                                                                                                              R (>= 3.4.0)
#> SummarizedExperiment                                                       R (>= 4.0.0), methods, MatrixGenerics (>= 1.1.3),\nGenomicRanges (>= 1.41.5), Biobase
#> summarytools                                                                                                                                         R (>= 2.10)
#> survey                                                                                                             R (>= 3.5.0), grid, methods, Matrix, survival
#> survminer                                                                                                                              ggplot2, ggpubr(>= 0.1.6)
#> survMisc                                                                                                                                                survival
#> sva                                                                                                                   R (>= 3.2), mgcv, genefilter, BiocParallel
#> svglite                                                                                                                                             R (>= 3.0.0)
#> sys                                                                                                                                                         <NA>
#> systemfonts                                                                                                                                         R (>= 3.2.0)
#> tableone                                                                                                                                                    <NA>
#> TCGAbiolinks                                                                                                                                          R (>= 4.0)
#> TCGAbiolinksGUI.data                                                                                                                                R (>= 3.5.0)
#> tensorflow                                                                                                                                            R (>= 3.1)
#> testextra                                                                                                                                                   <NA>
#> testthat                                                                                                                                              R (>= 3.1)
#> textshaping                                                                                                                                         R (>= 3.2.0)
#> tfautograph                                                                                                                                           R (>= 3.1)
#> tfruns                                                                                                                                                R (>= 3.1)
#> TH.data                                                                                                                             R (>= 3.5.0), survival, MASS
#> tibble                                                                                                                                              R (>= 3.1.0)
#> tictoc                                                                                                                                     R (>= 3.0.3), methods
#> tidygraph                                                                                                                                                   <NA>
#> tidyr                                                                                                                                                 R (>= 3.1)
#> tidyselect                                                                                                                                            R (>= 3.2)
#> tidytemplate                                                                                                                                                <NA>
#> tidytree                                                                                                                                            R (>= 3.4.0)
#> tidyverse                                                                                                                                             R (>= 3.3)
#> timeDate                                                                                                          R (>= 2.15.1), graphics, utils, stats, methods
#> tinytex                                                                                                                                                     <NA>
#> tmvnsim                                                                                                                                                     <NA>
#> treeio                                                                                                                                              R (>= 3.6.0)
#> TTR                                                                                                                                                         <NA>
#> tweenr                                                                                                                                              R (>= 3.2.0)
#> tzdb                                                                                                                                                R (>= 3.4.0)
#> UpSetR                                                                                                                                                R (>= 3.0)
#> usethis                                                                                                                                               R (>= 3.4)
#> utf8                                                                                                                                                 R (>= 2.10)
#> uuid                                                                                                                                                R (>= 2.9.0)
#> varSelRF                                                                                                                    R (>= 2.0.0), randomForest, parallel
#> vcd                                                                                                                                           R (>= 2.4.0), grid
#> vctrs                                                                                                                                                 R (>= 3.3)
#> VennDiagram                                                                                                        R (>= 3.5.0), grid (>= 2.14.1), futile.logger
#> VIM                                                                                                                                 R (>= 3.5.0),colorspace,grid
#> viridis                                                                                                                      R (>= 2.10), viridisLite (>= 0.4.0)
#> viridisLite                                                                                                                                          R (>= 2.10)
#> visdat                                                                                                                                              R (>= 3.2.2)
#> vroom                                                                                                                                                 R (>= 3.1)
#> waiter                                                                                                                                                      <NA>
#> waldo                                                                                                                                                       <NA>
#> webshot                                                                                                                                               R (>= 3.0)
#> whisker                                                                                                                                                     <NA>
#> withr                                                                                                                                               R (>= 3.2.0)
#> xfun                                                                                                                                                        <NA>
#> xgboost                                                                                                                                             R (>= 3.3.0)
#> xlsx                                                                                                                                                        <NA>
#> xlsxjars                                                                                                                                                   rJava
#> XML                                                                                                                                 R (>= 4.0.0), methods, utils
#> xml2                                                                                                                                                R (>= 3.1.0)
#> xopen                                                                                                                                                 R (>= 3.1)
#> xtable                                                                                                                                             R (>= 2.10.0)
#> xts                                                                                                                                              zoo (>= 1.7-12)
#> XVector                                                            R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>=\n0.27.12), IRanges (>= 2.23.9)
#> yaml                                                                                                                                                        <NA>
#> yulab.utils                                                                                                                                                 <NA>
#> zeallot                                                                                                                                                     <NA>
#> zip                                                                                                                                                         <NA>
#> zlibbioc                                                                                                                                                    <NA>
#> zoo                                                                                                                                          R (>= 3.1.0), stats
#> base                                                                                                                                                        <NA>
#> boot                                                                                                                               R (>= 3.0.0), graphics, stats
#> class                                                                                                                                 R (>= 3.0.0), stats, utils
#> cluster                                                                                                                                             R (>= 3.5.0)
#> codetools                                                                                                                                             R (>= 2.1)
#> compiler                                                                                                                                                    <NA>
#> datasets                                                                                                                                                    <NA>
#> foreign                                                                                                                                             R (>= 4.0.0)
#> graphics                                                                                                                                                    <NA>
#> grDevices                                                                                                                                                   <NA>
#> grid                                                                                                                                                        <NA>
#> KernSmooth                                                                                                                                   R (>= 2.5.0), stats
#> lattice                                                                                                                                             R (>= 3.0.0)
#> MASS                                                                                                             R (>= 3.3.0), grDevices, graphics, stats, utils
#> Matrix                                                                                                                                              R (>= 3.5.0)
#> methods                                                                                                                                                     <NA>
#> mgcv                                                                                                                              R (>= 3.6.0), nlme (>= 3.1-64)
#> nlme                                                                                                                                                R (>= 3.5.0)
#> nnet                                                                                                                                  R (>= 3.0.0), stats, utils
#> parallel                                                                                                                                                    <NA>
#> rpart                                                                                                                  R (>= 2.15.0), graphics, stats, grDevices
#> spatial                                                                                                                     R (>= 3.0.0), graphics, stats, utils
#> splines                                                                                                                                                     <NA>
#> stats                                                                                                                                                       <NA>
#> stats4                                                                                                                                                      <NA>
#> survival                                                                                                                                            R (>= 3.5.0)
#> tcltk                                                                                                                                                       <NA>
#> tools                                                                                                                                                       <NA>
#> utils                                                                                                                                                       <NA>
#>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Imports
#> abind                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   methods, utils
#> affy                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods,\npreprocessCore, stats, utils, zlibbioc
#> affyio                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               zlibbioc, methods
#> annotate                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Biobase, DBI, xtable, graphics, utils, stats, methods,\nBiocGenerics (>= 0.13.8), httr
#> AnnotationDbi                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST
#> ape                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 nlme, lattice, graphics, methods, stats, tools, utils,\nparallel, Rcpp (>= 0.12.0)
#> aplot                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ggfun (>= 0.0.6), ggplot2, ggplotify, patchwork, magrittr,\nmethods, utils
#> arm                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             abind, coda, graphics, grDevices, methods, nlme, utils
#> arules                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       stats, methods, generics, graphics, utils
#> askpass                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   sys (>= 2.1)
#> assertthat                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       tools
#> autokeras                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            keras, methods, reticulate, stats
#> backports                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> base64enc                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> BBmisc                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         checkmate (>= 1.8.0), data.table, methods, utils, stats
#> BH                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                <NA>
#> Biobase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        methods
#> BiocCheck                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        biocViews (>= 1.33.7), BiocManager, stringdist, graph, httr,\ntools, codetools, methods, utils, knitr
#> BiocFileCache                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              methods, stats, utils, dplyr, RSQLite, DBI, rappdirs,\nfilelock, curl, httr
#> BiocGenerics                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           methods, utils, graphics, stats
#> BiocManager                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      utils
#> Biocomb                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            rgl, MASS, e1071, randomForest, pROC, ROCR, arules, pamr,\nclass, nnet, rpart, FSelector, RWeka, grDevices, graphics,\nstats, utils
#> BiocParallel                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               stats, utils, futile.logger, parallel, snow
#> BiocStyle                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              bookdown, knitr (>= 1.30), rmarkdown (>= 1.2), stats, utils,\nyaml, BiocManager
#> BiocVersion                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> biocViews                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools,\nutils, XML, RCurl, RUnit, BiocManager
#> biomaRt                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       utils, XML (>= 3.99-0.7), AnnotationDbi, progress, stringr,\nhttr, digest, BiocFileCache, rappdirs, xml2
#> Biostrings                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          methods, utils, grDevices, graphics, stats, crayon
#> bit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               <NA>
#> bit64                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             <NA>
#> bitops                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            <NA>
#> blob                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  methods, rlang, vctrs (>= 0.2.1)
#> bookdown                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   htmltools (>= 0.3.6), knitr (>= 1.31), rmarkdown (>= 2.13),\njquerylib, xfun (>= 0.29), tinytex (>= 0.12), yaml (>= 2.1.19)
#> Boruta                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          ranger
#> bounceR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      purrr, furrr, parallel, mboost, strucchange, np, reshape2,\nggplot2, mRMRe, dplyr, future
#> brew                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> brio                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> broom                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 backports, dplyr (>= 1.0.0), ellipsis, generics (>= 0.0.2),\nglue, methods, purrr, rlang, stringr, tibble (>= 3.0.0), tidyr\n(>= 1.0.0), ggplot2
#> broom.helpers                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          broom, cli, dplyr, labelled, lifecycle, purrr, rlang (>=\n1.0.1), stats, stringr, tibble, tidyr
#> bslib                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         grDevices, htmltools (>= 0.5.2), jsonlite, sass (>= 0.4.0),\njquerylib (>= 0.1.3), rlang
#> C50                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        partykit, Cubist (>= 0.3.0)
#> cachem                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  rlang, fastmap
#> calibrate                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> callr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   processx (>= 3.5.0), R6, utils
#> car                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    abind, MASS, mgcv, nnet, pbkrtest (>= 0.4-4), quantreg,\ngrDevices, utils, stats, graphics, maptools, lme4 (>=\n1.1-27.1), nlme
#> carData                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           <NA>
#> caret                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         e1071, foreach, grDevices, methods, ModelMetrics (>= 1.2.2.2),\nnlme, plyr, pROC, recipes (>= 0.1.10), reshape2, stats, stats4,\nutils, withr (>= 2.0.0)
#> caTools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         bitops
#> cellranger                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             rematch, tibble
#> checkmate                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  backports (>= 1.1.0), utils
#> circlize                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          GlobalOptions (>= 0.1.2), shape, grDevices, utils, stats,\ncolorspace, methods, grid
#> classInt                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          grDevices, stats, graphics, e1071, class, KernSmooth
#> cli                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             glue (>= 1.6.0), utils
#> clipr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            utils
#> clue                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 stats, cluster, graphics, methods
#> clusterProfiler                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 AnnotationDbi, downloader, DOSE (>= 3.13.1), dplyr, enrichplot\n(>= 1.9.3), GO.db, GOSemSim, magrittr, methods, plyr, qvalue,\nrlang, stats, tidyr, utils, yulab.utils
#> coda                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           lattice
#> coin                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       methods, parallel, stats, stats4, utils, libcoin (>= 1.0-9),\nmatrixStats (>= 0.54.0), modeltools (>= 0.2-9), mvtnorm (>=\n1.0-5), multcomp
#> colorspace                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  graphics, grDevices, stats
#> combinat                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> commonmark                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        <NA>
#> ComplexHeatmap                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         circlize (>= 0.4.14), GetoptLong, colorspace, clue,\nRColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges,\nmatrixStats, foreach, doParallel, codetools
#> config                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                yaml (>= 2.1.19)
#> corrplot                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> cowplot                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ggplot2 (> 2.2.1), grid, gtable, grDevices, methods, rlang,\nscales
#> cpp11                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             <NA>
#> crayon                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       grDevices, methods, utils
#> credentials                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    openssl (>= 1.3), sys (>= 2.1), curl, jsonlite, askpass
#> crosstalk                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 htmltools (>= 0.3.6), jsonlite, lazyeval, R6
#> cubature                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Rcpp
#> Cubist                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 reshape2, utils
#> curl                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> cutpointr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           gridExtra (>= 2.2.1), foreach (>= 1.4.3), dplyr (>= 0.8.0),\ntidyselect (>= 1.1.0), tidyr (>= 1.0.0), purrr (>= 0.3.0),\ntibble (>= 3.0.0), ggplot2 (>= 3.0.0), Rcpp (>= 0.12.12),\nstats, utils, rlang (>= 0.4.0)
#> data.table                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     methods
#> DBI                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               <NA>
#> dbplyr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              assertthat (>= 0.2.0), blob (>= 1.2.0), DBI (>= 1.0.0), dplyr\n(>= 1.0.4), ellipsis, glue (>= 1.2.0), lifecycle (>= 1.0.0),\nmagrittr, methods, purrr (>= 0.2.5), R6 (>= 2.2.2), rlang (>=\n0.2.0), tibble (>= 1.4.2), tidyselect (>= 0.2.4), utils, vctrs,\nwithr
#> dbscan                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Rcpp (>= 1.0.0), graphics, stats
#> deepnet                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           <NA>
#> DelayedArray                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     stats
#> DEoptimR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         stats
#> Deriv                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          methods
#> desc                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         cli, R6, rprojroot, utils
#> DESeq2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    BiocGenerics (>= 0.7.5), Biobase, BiocParallel, genefilter,\nmethods, stats4, locfit, geneplotter, ggplot2, Rcpp (>= 0.11.0)
#> devtools                                                                                                                                                                                                                                                                                                                                                                                             callr (>= 3.6.0), cli (>= 3.0.0), desc (>= 1.3.0), ellipsis\n(>= 0.3.1), fs (>= 1.5.0), httr (>= 1.4.2), lifecycle (>=\n1.0.0), memoise (>= 2.0.0), pkgbuild (>= 1.2.0), pkgload (>=\n1.2.1), rcmdcheck (>= 1.3.3), remotes (>= 2.3.0), rlang (>=\n0.4.10), roxygen2 (>= 7.1.1), rstudioapi (>= 0.13), rversions\n(>= 2.0.2), sessioninfo (>= 1.1.1), stats, testthat (>= 3.0.2),\ntools, utils, withr (>= 2.4.1)
#> DiceKriging                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> diffobj                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                crayon (>= 1.3.2), tools, methods, utils, stats
#> digest                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           utils
#> DMwR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        xts (>= 0.6-7), quantmod (>= 0.3-8), zoo (>= 1.6-4), abind (>=\n1.1-0), rpart (>= 3.1-46), class (>= 7.3-1), ROCR (>= 1.0)
#> DO.db                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           methods, AnnotationDbi
#> doParallel                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        <NA>
#> DOSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 AnnotationDbi, BiocParallel, DO.db, fgsea, ggplot2, GOSemSim\n(>= 2.0.0), methods, qvalue, reshape2, stats, utils
#> downlit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              brio, desc, digest, evaluate, fansi, memoise, rlang, vctrs,\nyaml
#> downloader                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               utils, digest
#> dplyr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       generics, glue (>= 1.3.2), lifecycle (>= 1.0.1), magrittr (>=\n1.5), methods, R6, rlang (>= 1.0.2), tibble (>= 2.1.3),\ntidyselect (>= 1.1.1), utils, vctrs (>= 0.4.1), pillar (>=\n1.5.1)
#> DT                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         htmltools (>= 0.3.6), htmlwidgets (>= 1.3), jsonlite (>=\n0.9.16), magrittr, crosstalk, jquerylib, promises
#> dtplyr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  crayon, data.table (>= 1.13.0), dplyr (>= 1.0.3), ellipsis,\nglue, lifecycle, rlang, tibble, tidyselect, vctrs
#> e1071                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         graphics, grDevices, class, stats, methods, utils, proxy
#> edgeR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    methods, graphics, stats, utils, locfit, Rcpp
#> ellipsis                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              rlang (>= 0.3.0)
#> enrichplot                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 aplot, DOSE (>= 3.16.0), ggplot2, ggraph, graphics, grid,\nigraph, methods, plyr, purrr, RColorBrewer, reshape2, stats,\nutils, scatterpie, shadowtext, GOSemSim, magrittr, ggtree,\nyulab.utils (>= 0.0.4)
#> entropy                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           <NA>
#> epiDisplay                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        <NA>
#> evaluate                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       methods
#> exactRankTests                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    <NA>
#> fansi                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 grDevices, utils
#> farver                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            <NA>
#> fastmap                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           <NA>
#> fastmatch                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> feseR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             caret, e1071, randomForest, FSelector, plyr, ggbiplot,\nggplot2, corrplot, ROCR, foreach, doParallel
#> fgsea                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Rcpp, data.table, BiocParallel, stats, ggplot2 (>= 2.2.0),\ngridExtra, grid, fastmatch, Matrix, utils
#> filelock                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> fontawesome                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  rlang (>= 0.4.10), htmltools (>= 0.5.1.1)
#> forcats                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ellipsis, magrittr, rlang, tibble
#> foreach                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    codetools, utils, iterators
#> formatR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           <NA>
#> Formula                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           <NA>
#> fs                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             methods
#> FSelector                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         digest, entropy, randomForest, RWeka
#> funModeling                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ROCR, ggplot2, gridExtra, pander, reshape2, scales, dplyr,\nlazyeval, utils, RColorBrewer, moments, entropy, cli, stringr
#> furrr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 globals (>= 0.14.0), lifecycle (>= 1.0.1), purrr (>= 0.3.4),\nrlang (>= 1.0.2), vctrs (>= 0.4.1)
#> futile.logger                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               utils, lambda.r (>= 1.1.0), futile.options
#> futile.options                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    <NA>
#> future                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                digest, globals (>= 0.15.0), listenv (>= 0.8.0), parallel,\nparallelly (>= 1.30.0), tools, utils
#> future.apply                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      globals (>= 0.14.0), parallel, utils
#> gargle                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        cli (>= 3.0.0), fs (>= 1.3.1), glue (>= 1.3.0), httr (>=\n1.4.0), jsonlite, rappdirs, rlang (>= 0.4.9), rstudioapi,\nstats, utils, withr
#> gdata                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    gtools, stats, methods, utils
#> GDCRNATools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2,\nclusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival,\nsurvminer, pathview, ggplot2, gplots, DT, GenomicDataCommons,\nBiocParallel
#> genefilter                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              BiocGenerics, AnnotationDbi, annotate, Biobase, graphics,\nmethods, stats, survival, grDevices
#> geneplotter                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats,\nutils
#> generics                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       methods
#> GenomeInfoDb                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             stats, stats4, utils, RCurl, GenomeInfoDbData
#> GenomeInfoDbData                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  <NA>
#> GenomicDataCommons                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  stats, httr, xml2, jsonlite, utils, rlang, readr,\nGenomicRanges, IRanges, dplyr, rappdirs, tibble
#> GenomicRanges                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        utils, stats, XVector (>= 0.29.2)
#> gert                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   askpass, credentials (>= 1.2.1), openssl (>= 1.4.1),\nrstudioapi (>= 0.11), sys, zip (>= 2.1.0)
#> GetoptLong                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            rjson, GlobalOptions (>= 0.1.0), methods, crayon
#> ggbiplot                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> ggforce                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Rcpp (>= 0.12.2), grid, scales, MASS, tweenr (>= 0.1.5),\ngtable, rlang, polyclip, stats, grDevices, tidyselect, withr,\nutils
#> ggfun                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ggplot2, grid, rlang, utils
#> ggplot2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 digest, glue, grDevices, grid, gtable (>= 0.1.1), isoband,\nMASS, mgcv, rlang (>= 0.4.10), scales (>= 0.5.0), stats,\ntibble, withr (>= 2.0.0)
#> ggplotify                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                ggplot2, graphics, grDevices, grid, gridGraphics, yulab.utils
#> ggpubr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          ggrepel, grid, ggsci, stats, utils, tidyr, purrr, dplyr (>=\n0.7.1), cowplot, ggsignif, scales, gridExtra, glue, polynom,\nrlang, rstatix (>= 0.6.0), tibble, magrittr
#> ggraph                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Rcpp (>= 0.12.2), dplyr, ggforce (>= 0.3.1), grid, igraph (>=\n1.0.0), scales, MASS, digest, gtable, ggrepel, utils, stats,\nviridis, rlang, tidygraph, graphlayouts (>= 0.5.0), withr
#> ggrepel                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                grid, Rcpp, rlang (>= 0.3.0), scales (>= 0.5.0)
#> ggsci                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            grDevices, scales, ggplot2 (>= 2.0.0)
#> ggsignif                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ggplot2 (>= 3.3.5)
#> ggtext                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               ggplot2 (>= 3.3.0), grid, gridtext, rlang, scales
#> ggtree                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ape, aplot, dplyr, ggplot2 (>= 3.0.0), grid, magrittr,\nmethods, purrr, rlang, ggfun (>= 0.0.6), yulab.utils, tidyr,\ntidytree (>= 0.3.9), treeio (>= 1.8.0), utils, scales
#> gh                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              cli (>= 2.0.1), gitcreds, httr (>= 1.2), ini, jsonlite
#> gitcreds                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> gld                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       stats, graphics, e1071, lmom
#> glmnet                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  methods, utils, foreach, shape, survival, Rcpp
#> GlobalOptions                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    utils
#> globals                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      codetools
#> glue                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           methods
#> gmodels                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    MASS, gdata
#> GO.db                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             <NA>
#> googledrive                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            cli (>= 3.0.0), gargle (>= 1.2.0), glue (>= 1.4.2), httr,\njsonlite, lifecycle, magrittr, pillar, purrr (>= 0.2.3), rlang\n(>= 0.4.9), tibble (>= 2.0.0), utils, uuid, vctrs (>= 0.3.0),\nwithr
#> googlesheets4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            cellranger, cli (>= 3.0.0), curl, gargle (>= 1.2.0), glue (>=\n1.3.0), googledrive (>= 2.0.0), httr, ids, magrittr, methods,\npurrr, rematch2, rlang (>= 0.4.11), tibble (>= 2.1.1), utils,\nvctrs (>= 0.2.3)
#> GOSemSim                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          AnnotationDbi, GO.db, methods, utils
#> gower                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             <NA>
#> gplots                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     gtools, stats, caTools, KernSmooth, methods
#> graph                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             stats, stats4, utils
#> graphlayouts                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              igraph, Rcpp
#> gridExtra                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     gtable, grid, grDevices, graphics, utils
#> gridGraphics                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 grDevices
#> gridtext                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      grid, grDevices, markdown, rlang, Rcpp, RCurl, png, jpeg,\nstringr, xml2
#> gt                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         base64enc (>= 0.1-3), bitops (>= 1.0.6), checkmate (>= 2.0.0),\ncommonmark (>= 1.7), dplyr (>= 1.0.8), fs (>= 1.5.2), ggplot2\n(>= 3.3.5), glue (>= 1.6.1), htmltools (>= 0.5.2), magrittr (>=\n2.0.2), rlang (>= 1.0.1), sass (>= 0.4.0), scales (>= 1.1.1),\nstringr (>= 1.4.0), tibble (>= 3.1.6), tidyselect (>= 1.1.1)
#> gtable                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            grid
#> gtools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            <NA>
#> gtsummary                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    broom (>= 0.8.0), broom.helpers (>= 1.7.0), cli (>= 3.1.1),\ndplyr (>= 1.0.7), forcats (>= 0.5.1), glue (>= 1.6.0), gt (>=\n0.5.0), knitr (>= 1.37), lifecycle (>= 1.0.1), purrr (>=\n0.3.4), rlang (>= 0.4.12), stringr (>= 1.4.0), tibble (>=\n3.1.6), tidyr (>= 1.1.4)
#> hardhat                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               glue, rlang (>= 0.4.2), tibble, vctrs (>= 0.3.0)
#> hash                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> haven                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          cli (>= 3.0.0), forcats (>= 0.2.0), hms, lifecycle, methods,\nreadr (>= 0.1.0), rlang (>= 0.4.0), tibble, tidyselect, vctrs\n(>= 0.3.0)
#> here                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              rprojroot (>= 2.0.2)
#> highr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   xfun (>= 0.18)
#> Hmisc                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                methods, latticeExtra, cluster, rpart, nnet, foreign, gtable,\ngrid, gridExtra, data.table, htmlTable (>= 1.11.0), viridis,\nhtmltools, base64enc
#> hms                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ellipsis (>= 0.3.2), lifecycle, methods, pkgconfig, rlang,\nvctrs (>= 0.3.8)
#> htmlTable                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 stringr, knitr (>= 1.6), magrittr (>= 1.5), methods,\ncheckmate, htmlwidgets, htmltools, rstudioapi (>= 0.6)
#> htmltools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             utils, digest, grDevices, base64enc, rlang (>= 0.4.10),\nfastmap
#> htmlwidgets                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  grDevices, htmltools (>= 0.3), jsonlite (>= 0.9.16), yaml
#> HTqPCR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 affy, Biobase, gplots, graphics, grDevices, limma, methods,\nRColorBrewer, stats, stats4, utils
#> httpuv                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Rcpp (>= 1.0.7), utils, R6, promises, later (>= 0.8.0)
#> httr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             curl (>= 3.0.0), jsonlite, mime, openssl (>= 0.8), R6
#> ids                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      openssl, uuid
#> igraph                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      graphics, grDevices, magrittr, Matrix, pkgconfig (>= 2.0.0),\nstats, utils
#> imputeMissings                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      randomForest,stats
#> ini                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               <NA>
#> inum                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         stats, libcoin (>= 1.0-0)
#> ipred                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           rpart (>= 3.1-8), MASS, survival, nnet, class, prodlim
#> IRanges                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         stats4
#> isoband                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    grid, utils
#> iterators                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> jpeg                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> jquerylib                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    htmltools
#> jsonlite                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> kableExtra                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 knitr (>= 1.16), magrittr, stringr (>= 1.0), xml2 (>= 1.1.1),\nrvest, rmarkdown (>= 1.6.0), scales, viridisLite, stats,\ngrDevices, htmltools, rstudioapi, glue, tools, webshot, digest,\ngraphics, svglite
#> KEGGgraph                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      methods, XML (>= 2.3-0), graph, utils, RCurl, Rgraphviz
#> KEGGREST                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                methods, httr, png, Biostrings
#> keras                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        generics (>= 0.0.1), reticulate (> 1.22), tensorflow (>=\n2.8.0), tfruns (>= 1.0), magrittr, zeallot, glue, methods, R6,\nellipsis, rlang
#> kernlab                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            methods, stats, grDevices, graphics
#> klaR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            combinat, questionr, grDevices, stats, utils, graphics
#> km.ci                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  stats, survival
#> KMsurv                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            <NA>
#> knitr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   evaluate (>= 0.15), highr, methods, stringr (>= 0.6), yaml (>=\n2.1.19), xfun (>= 0.29), tools
#> labeling                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               stats, graphics
#> labelled                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  haven (>= 2.4.1), dplyr (>= 1.0.0), lifecycle, rlang, vctrs,\nstringr, tidyr
#> laeken                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      boot, MASS
#> lambda.r                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       formatR
#> later                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Rcpp (>= 0.12.9), rlang
#> latticeExtra                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    grid, stats, utils, grDevices, png, jpeg, RColorBrewer
#> lava                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 future.apply, progressr, grDevices, graphics, methods,\nnumDeriv, stats, survival, SQUAREM, utils
#> lavaan                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      methods, stats4, stats, utils, graphics, MASS, mnormt,\npbivnorm, numDeriv
#> lazyeval                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> lhs                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Rcpp
#> libcoin                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 stats, mvtnorm
#> lifecycle                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      glue, rlang (>= 0.4.10)
#> limma                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       grDevices, graphics, stats, utils, methods
#> listenv                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           <NA>
#> lme4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           graphics, grid, splines, utils, parallel, MASS, lattice, boot,\nnlme (>= 3.1-123), minqa (>= 1.1.15), nloptr (>= 1.0.4)
#> lmom                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   stats, graphics
#> lmtest                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        graphics
#> lobstr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  crayon, Rcpp, rlang (>= 0.3.0)
#> locfit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         lattice
#> lubridate                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     generics
#> magick                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Rcpp (>= 0.12.12), magrittr, curl
#> magrittr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> maptools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            foreign (>= 0.8), methods, grid, lattice, stats, utils,\ngrDevices
#> markdown                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    utils, xfun, mime (>= 0.3)
#> MatchIt                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          backports (>= 1.1.9), Rcpp (>= 1.0.7)
#> MatrixGenerics                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 methods
#> MatrixModels                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         stats, methods, Matrix (>= 1.1-5)
#> matrixStats                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> maxstat                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 exactRankTests(>= 0.8-23), mvtnorm(>= 0.5-10), stats, graphics
#> mboost                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Matrix, survival (>= 3.2-10), splines, lattice, nnls,\nquadprog, utils, graphics, grDevices, partykit (>= 1.2-1)
#> memoise                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      rlang (>= 0.4.10), cachem
#> mice                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           broom, dplyr, generics, graphics, grDevices, lattice, methods,\nRcpp, rlang, stats, tidyr, utils, withr
#> mime                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             tools
#> miniUI                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      shiny (>= 0.13), htmltools (>= 0.3), utils
#> minqa                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Rcpp (>= 0.9.10)
#> mitools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            DBI, methods, stats
#> mlbench                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           <NA>
#> mlr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               backports (>= 1.1.0), BBmisc (>= 1.11), checkmate (>= 1.8.2),\ndata.table (>= 1.12.4), ggplot2, methods, parallelMap (>= 1.3),\nstats, stringi, survival, utils, XML
#> mnormt                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              tmvnsim (>= 1.0-2)
#> ModelMetrics                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Rcpp, data.table
#> modelr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               broom, magrittr, purrr (>= 0.2.2), rlang (>= 0.2.0), tibble,\ntidyr (>= 0.8.0), tidyselect, vctrs
#> modeltools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     methods
#> moments                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           <NA>
#> mRMRe                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             <NA>
#> multcomp                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                sandwich (>= 2.3-0), codetools
#> munsell                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            colorspace, methods
#> mvtnorm                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 stats, methods
#> My.stepwise                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               car, lmtest, survival, stats
#> naniar                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          dplyr, ggplot2, purrr, tidyr, tibble (>= 2.0.0), norm,\nmagrittr, stats, visdat, rlang, forcats, viridis, glue, UpSetR
#> networkD3                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     htmlwidgets (>= 0.3.2), igraph, magrittr
#> nloptr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            <NA>
#> nnls                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> nondetects                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     limma, mvtnorm, utils, methods, arm, HTqPCR (>= 1.16.0)
#> norm                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             stats
#> np                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  boot, cubature, methods, quadprog, quantreg, stats
#> numDeriv                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> OmicSelector            dplyr, snow, remotes, devtools, ellipsis, BiocManager, plyr,\ntibble, tidyr, XML, epiDisplay, rsq, MASS, caret, tidyverse,\nxtable, pROC, ggplot2, DMwR, ROSE, gridExtra, gplots, stringr,\ndata.table, doParallel, Boruta, spFSR, varSelRF, My.stepwise,\npsych, C50, randomForest, nnet, reticulate, stargazer, ggrepel,\nclassInt, plotly, keras, cutpointr, naniar, visdat,\nimputeMissings, foreach, deepnet, calibrate, networkD3,\nVennDiagram, RSNNS, kernlab, car, PairedData, profileR,\nxgboost, kableExtra, curl, tidyselect, rJava, mice, MatchIt,\ncluster, Biobase, Biocomb, ComplexHeatmap, GDCRNATools,\nR.utils, TCGAbiolinks, VIM, circlize, edgeR, magick, mgcv,\nparty, rmarkdown, rpart, sva, devtools, nnet, klaR,\nParBayesianOptimization, recipes, resample, mlbench
#> openssl                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        askpass
#> org.Hs.eg.db                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> PairedData                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        <NA>
#> pamr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> pander                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                grDevices, graphics, methods, utils, stats, digest, tools,\nRcpp
#> parallelly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      parallel, tools, utils
#> parallelMap                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              BBmisc (>= 1.8), checkmate (>= 1.8.0), parallel, stats, utils
#> ParamHelpers                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    backports, BBmisc (>= 1.10), checkmate (>= 1.8.2), fastmatch,\nmethods
#> ParBayesianOptimization                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          data.table (>= 1.11.8), DiceKriging, stats, foreach, dbscan,\nlhs, crayon, ggplot2, ggpubr (>= 0.2.4)
#> parsetools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              methods, utils
#> party                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 survival (>= 2.37-7), coin (>= 1.1-0), zoo, sandwich (>=\n1.1-1)
#> partykit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    grDevices, stats, utils, survival, Formula (>= 1.2-1), inum\n(>= 1.0-0), rpart (>= 4.1-11)
#> patchwork                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         ggplot2 (>= 3.0.0), gtable, grid, stats, grDevices, utils,\ngraphics
#> pathview                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi,\norg.Hs.eg.db, KEGGREST, methods, utils
#> pbivnorm                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> pbkrtest                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          broom, dplyr, magrittr, MASS, Matrix (>= 1.2.3), methods,\nnumDeriv, parallel, knitr
#> pillar                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    cli (>= 2.3.0), crayon (>= 1.3.4), ellipsis (>= 0.3.2), fansi,\nglue, lifecycle, rlang (>= 0.3.0), utf8 (>= 1.1.0), utils,\nvctrs (>= 0.3.8)
#> pkgbuild                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            callr (>= 3.2.0), cli, crayon, desc, prettyunits, R6,\nrprojroot, withr (>= 2.3.0)
#> pkgcond                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            assertthat, methods
#> pkgconfig                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        utils
#> pkgdown                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                bslib (>= 0.3.1), callr (>= 2.0.2), crayon, desc, digest,\ndownlit (>= 0.4.0), fs (>= 1.4.0), httr (>= 1.4.2), jsonlite,\nmagrittr, memoise, purrr, ragg, rlang (>= 1.0.0), rmarkdown (>=\n1.1.9007), tibble, whisker, withr (>= 2.4.3), xml2 (>= 1.3.1),\nyaml
#> pkgload                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        cli, crayon, desc, methods, rlang, rprojroot, rstudioapi,\nutils, withr
#> plogr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             <NA>
#> plotly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        tools, scales, httr (>= 1.3.0), jsonlite (>= 1.6), magrittr,\ndigest, viridisLite, base64enc, htmltools (>= 0.3.6),\nhtmlwidgets (>= 1.5.2.9001), tidyr (>= 1.0.0), RColorBrewer,\ndplyr, vctrs, tibble, lazyeval (>= 0.2.0), rlang (>= 0.4.10),\ncrosstalk, purrr, data.table, promises
#> plyr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Rcpp (>= 0.11.0)
#> png                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               <NA>
#> polspline                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              stats, graphics
#> polyclip                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> polynom                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                stats, graphics
#> postlogic                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> praise                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            <NA>
#> preprocessCore                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   stats
#> prettyunits                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> pROC                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   methods, plyr, Rcpp (>= 0.11.1)
#> processx                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ps (>= 1.2.0), R6, utils
#> prodlim                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Rcpp (>= 0.11.5), stats, grDevices, graphics, survival,\nKernSmooth, lava
#> profileR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> progress                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  hms, prettyunits, R6, crayon
#> progressr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                digest, utils
#> promises                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       R6, Rcpp, later, rlang, stats, magrittr
#> proxy                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     stats, utils
#> pryr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             stringr, codetools, methods, Rcpp (>= 0.11.0), lobstr
#> ps                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               utils
#> psych                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    mnormt,parallel,stats,graphics,grDevices,methods,lattice,nlme
#> purrr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              magrittr (>= 1.5), rlang (>= 0.3.1)
#> purrrogress                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               R6, assertthat, glue, hms, methods, pkgcond, purrr, testextra,\nutils, rlang
#> quadprog                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> quantmod                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          curl
#> quantreg                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       methods, graphics, Matrix, MatrixModels, survival, MASS
#> questionr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       shiny (>= 1.0.5), miniUI, rstudioapi, highr, styler, classInt,\nhtmltools, graphics, stats, utils, labelled (>= 2.6.0)
#> qvalue                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                splines, ggplot2, grid, reshape2
#> R.cache                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      utils, R.methodsS3 (>= 1.8.1), R.oo (>= 1.24.0), R.utils (>=\n2.10.1), digest (>= 0.6.13)
#> R.methodsS3                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      utils
#> R.oo                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    methods, utils
#> R.utils                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  methods, utils, tools, R.methodsS3 (>= 1.8.1)
#> R6                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                <NA>
#> ragg                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    systemfonts (>= 1.0.3), textshaping (>= 0.3.0)
#> randomForest                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> ranger                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Rcpp (>= 0.11.2), Matrix
#> RANN                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> rappdirs                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> rapportools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               plyr, pander, reshape2, MASS
#> RBGL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           methods
#> rcmdcheck                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    callr (>= 3.1.1.9000), cli (>= 3.0.0), curl, desc (>= 1.2.0),\ndigest, pkgbuild, prettyunits, R6, rprojroot, sessioninfo (>=\n1.1.1), utils, withr, xopen
#> RColorBrewer                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> Rcpp                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    methods, utils
#> RcppArmadillo                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Rcpp (>= 0.11.0), stats, utils, methods
#> RcppEigen                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Matrix (>= 1.1-0), Rcpp (>= 0.11.0), stats, utils
#> RcppProgress                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> RcppTOML                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Rcpp (>= 0.11.5)
#> RCurl                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           bitops
#> readr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        cli (>= 3.0.0), clipr, crayon, hms (>= 0.4.1), lifecycle (>=\n0.2.0), methods, R6, rlang, tibble, utils, vroom (>= 1.5.6)
#> readxl                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            cellranger, tibble (>= 2.0.1), utils
#> recipes                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             ellipsis, generics (>= 0.1.0.9000), glue, gower, hardhat (>=\n0.1.6.9001), ipred (>= 0.9-12), lifecycle, lubridate, magrittr,\nMatrix, purrr (>= 0.2.3), rlang (>= 0.4.0), stats, tibble,\ntidyr (>= 1.0.0), tidyselect (>= 1.1.0), timeDate, utils,\nvctrs, withr
#> rematch                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           <NA>
#> rematch2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        tibble
#> remotes                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   methods, stats, tools, utils
#> reprex                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               callr (>= 3.6.0), cli (>= 2.3.1), clipr (>= 0.4.0), fs, glue,\nknitr (>= 1.23), rlang (>= 0.4.0), rmarkdown, rstudioapi,\nutils, withr (>= 2.3.0)
#> resample                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> reshape                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           plyr
#> reshape2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                plyr (>= 1.8.1), Rcpp, stringr
#> reticulate                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Matrix, Rcpp (>= 0.12.7), RcppTOML, graphics, here, jsonlite,\nmethods, png, rappdirs, utils, withr
#> rgl                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    graphics, grDevices, stats, utils, htmlwidgets, htmltools,\nknitr (>= 1.33), jsonlite (>= 0.9.20), magrittr, R6
#> Rgraphviz                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  stats4, graphics, grDevices
#> rhandsontable                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               jsonlite, htmlwidgets (>= 0.3.3), magrittr, methods, utils
#> rJava                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             <NA>
#> rjson                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             <NA>
#> rlang                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            utils
#> rmarkdown                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        bslib (>= 0.2.5.1), evaluate (>= 0.13), htmltools (>= 0.3.5),\njquerylib, jsonlite, knitr (>= 1.22), methods, stringr (>=\n1.2.0), tinytex (>= 0.31), tools, utils, xfun (>= 0.30), yaml\n(>= 2.1.19)
#> rms                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        methods, quantreg, rpart, nlme (>= 3.1-123), polspline,\nmultcomp, htmlTable (>= 1.11.0), htmltools, MASS, cluster,\ndigest
#> robustbase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   stats, graphics, utils, methods, DEoptimR
#> ROCR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       methods, graphics, grDevices, gplots, stats
#> ROSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> roxygen2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          brew, cli (>= 3.3.0), commonmark, desc (>= 1.2.0), digest,\nknitr, methods, pkgload (>= 1.0.2), purrr (>= 0.3.3), R6 (>=\n2.1.2), rlang (>= 1.0.0), stringi, stringr (>= 1.0.0), utils,\nwithr, xml2
#> rprojroot                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> RSNNS                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             <NA>
#> rsq                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    methods, stats, MASS, lme4, nlme, Deriv, Matrix
#> RSQLite                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          bit64, blob (>= 1.2.0), DBI (>= 1.1.0), memoise, methods,\npkgconfig, Rcpp (>= 1.0.7)
#> rstatix                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          stats, utils, tidyr (>= 1.0.0), purrr, broom (>= 0.7.4), rlang\n(>= 0.3.1), tibble (>= 2.1.3), dplyr (>= 0.7.1), magrittr,\ncorrplot, tidyselect (>= 1.0.0), car, generics (>= 0.0.2)
#> rstudioapi                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        <NA>
#> RUnit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             <NA>
#> rversions                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 curl, utils, xml2 (>= 1.0.0)
#> rvest                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                httr (>= 0.5), lifecycle (>= 1.0.0), magrittr, rlang (>=\n0.4.10), selectr, tibble, xml2 (>= 1.3)
#> RWeka                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          RWekajars (>= 3.9.3-1), rJava (>= 0.6-3), graphics, stats,\nutils, grid
#> RWekajars                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             rJava (>= 0.6-3)
#> S4Vectors                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> sandwich                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             stats, utils, zoo
#> sass                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         fs, rlang (>= 0.4.10), htmltools (>= 0.5.1), R6, rappdirs
#> scales                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      farver (>= 2.0.3), labeling, lifecycle, munsell (>= 0.5), R6,\nRColorBrewer, rlang (>= 1.0.0), viridisLite
#> scatterpie                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ggforce, rlang, ggfun, stats, tidyr, utils
#> selectr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           methods, stringr, R6
#> sessioninfo                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               cli (>= 3.1.0), tools, utils
#> shadowtext                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ggplot2, grid, scales
#> shape                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       stats, graphics, grDevices
#> shiny                                                                                                                                                                                                                                                                                                                                                                                                                                                utils, grDevices, httpuv (>= 1.5.2), mime (>= 0.3), jsonlite\n(>= 0.9.16), xtable, fontawesome (>= 0.2.1), htmltools (>=\n0.5.2), R6 (>= 2.0), sourcetools, later (>= 1.0.0), promises\n(>= 1.1.0), tools, crayon, rlang (>= 0.4.10), fastmap (>=\n1.1.0), withr, commonmark (>= 1.7), glue (>= 1.3.2), bslib (>=\n0.3.0), cachem, ellipsis, lifecycle (>= 0.2.0)
#> shinyfullscreen                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        shiny, jsonlite
#> shinyjqui                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    shiny (>= 1.5.0), htmltools, htmlwidgets, jsonlite, rlang
#> shinyjs                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  digest (>= 0.6.8), jsonlite, shiny (>= 1.0.0)
#> snow                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> sourcetools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> sp                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    utils, stats, graphics, grDevices, lattice, grid
#> SparseM                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         graphics, stats, utils
#> spFSR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             ggplot2 (>= 2.2.1), class (>= 7.3), mlbench (>= 2.1)
#> SQUAREM                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           <NA>
#> stabs                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       graphics, grDevices, utils
#> stargazer                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 stats, utils
#> stringdist                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    parallel
#> stringi                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            tools, utils, stats
#> stringr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  glue (>= 1.2.0), magrittr, stringi (>= 1.1.7)
#> strucchange                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     graphics, stats, utils
#> styler                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            cli (>= 3.1.1), magrittr (>= 2.0.0), purrr (>= 0.2.3), R.cache\n(>= 0.15.0), rematch2 (>= 2.0.1), rlang (>= 0.1.1), rprojroot\n(>= 1.1), tibble (>= 1.4.2), tools, withr (>= 1.0.0),
#> SummarizedExperiment                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          utils, stats, tools, Matrix, BiocGenerics (>= 0.37.0),\nS4Vectors (>= 0.33.7), IRanges (>= 2.23.9), GenomeInfoDb (>=\n1.13.1), DelayedArray (>= 0.15.10)
#> summarytools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               base64enc, checkmate, dplyr, grDevices, htmltools, lubridate,\nmagick, matrixStats, methods, pander, pryr, rapportools, stats,\ntcltk, tibble, tidyr, utils
#> survey                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           stats, graphics, splines, lattice, minqa, numDeriv, mitools\n(>= 2.4)
#> survminer                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      grid, gridExtra (>= 2.0), magrittr, maxstat, methods, scales,\nsurvival, stats, broom, dplyr, tidyr, survMisc, purrr, tibble,\nrlang, ggtext (>= 0.1.0)
#> survMisc                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   graphics, grDevices, stats, utils, knitr, KMsurv, ggplot2,\ndata.table, zoo, grid, gridExtra, km.ci, xtable
#> sva                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  matrixStats, stats, graphics, utils, limma, edgeR
#> svglite                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         systemfonts (>= 1.0.0)
#> sys                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               <NA>
#> systemfonts                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> tableone                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             survey, MASS, e1071, zoo, gmodels, nlme, labelled
#> TCGAbiolinks                                                                                                                                                                                                                                                                                                                                                                                                                              downloader (>= 0.4), grDevices, biomaRt, dplyr, graphics,\ntibble, GenomicRanges, XML (>= 3.98.0), data.table, jsonlite\n(>= 1.0.0), plyr, knitr, methods, ggplot2, stringr (>= 1.0.0),\nIRanges, rvest (>= 0.3.0), stats, utils, S4Vectors, R.utils,\nSummarizedExperiment (>= 1.4.0), TCGAbiolinksGUI.data (>=\n1.15.1), readr, tools, tidyr, purrr, xml2, httr (>= 1.2.1)
#> TCGAbiolinksGUI.data                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> tensorflow                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              config, processx, reticulate (>= 1.24), tfruns (>= 1.0),\nutils, yaml, grDevices, tfautograph (>= 0.3.1), rstudioapi (>=\n0.7)
#> testextra                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 assertthat, methods, parsetools, pkgcond, postlogic, purrr,\nrlang, stringi, testthat, utils
#> testthat                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      brio, callr (>= 3.5.1), cli (>= 3.3.0), crayon (>= 1.3.4),\ndesc, digest, ellipsis (>= 0.2.0), evaluate, jsonlite,\nlifecycle, magrittr, methods, pkgload, praise, processx, ps (>=\n1.3.4), R6 (>= 2.2.0), rlang (>= 1.0.1), utils, waldo (>=\n0.4.0), withr (>= 2.4.3)
#> textshaping                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     systemfonts (>= 1.0.0)
#> tfautograph                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      reticulate, backports
#> tfruns                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       utils, jsonlite (>= 1.2), base64enc, yaml, config, magrittr,\nwhisker, tidyselect, rlang, rstudioapi (>= 0.7), reticulate
#> TH.data                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           <NA>
#> tibble                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ellipsis (>= 0.3.2), fansi (>= 0.4.0), lifecycle (>= 1.0.0),\nmagrittr, methods, pillar (>= 1.7.0), pkgconfig, rlang (>=\n1.0.1), utils, vctrs (>= 0.3.8)
#> tictoc                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            <NA>
#> tidygraph                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              tibble, dplyr (>= 0.8.5), igraph, magrittr, utils, rlang, R6,\ntools, stats, tidyr, pillar, cli
#> tidyr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              dplyr (>= 1.0.0), ellipsis (>= 0.1.0), glue, lifecycle,\nmagrittr, purrr, rlang, tibble (>= 2.1.1), tidyselect (>=\n1.1.0), utils, vctrs (>= 0.3.7)
#> tidyselect                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ellipsis, glue (>= 1.3.0), purrr (>= 0.3.2), rlang (>= 1.0.1),\nvctrs (>= 0.3.0)
#> tidytemplate                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> tidytree                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    ape, dplyr, lazyeval, magrittr, methods, rlang, tibble, tidyr,\ntidyselect, yulab.utils (>= 0.0.4), pillar
#> tidyverse                                                                                                                                                                                                                      broom (>= 0.7.6), cli (>= 2.4.0), crayon (>= 1.4.1), dbplyr\n(>= 2.1.1), dplyr (>= 1.0.5), dtplyr (>= 1.1.0), forcats (>=\n0.5.1), googledrive (>= 1.0.1), googlesheets4 (>= 0.3.0),\nggplot2 (>= 3.3.3), haven (>= 2.3.1), hms (>= 1.0.0), httr (>=\n1.4.2), jsonlite (>= 1.7.2), lubridate (>= 1.7.10), magrittr\n(>= 2.0.1), modelr (>= 0.1.8), pillar (>= 1.6.0), purrr (>=\n0.3.4), readr (>= 1.4.0), readxl (>= 1.3.1), reprex (>= 2.0.0),\nrlang (>= 0.4.10), rstudioapi (>= 0.13), rvest (>= 1.0.0),\nstringr (>= 1.4.0), tibble (>= 3.1.0), tidyr (>= 1.1.3), xml2\n(>= 1.3.2)
#> timeDate                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> tinytex                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 xfun (>= 0.29)
#> tmvnsim                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           <NA>
#> treeio                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             ape, dplyr, jsonlite, magrittr, methods, rlang, tibble,\ntidytree (>= 0.3.9), utils
#> TTR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         xts (>= 0.10-0), zoo, curl
#> tweenr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Rcpp (>= 0.12.3), grDevices, farver, magrittr, rlang
#> tzdb                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> UpSetR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             ggplot2, gridExtra, plyr, utils, stats, methods, grDevices,\nscales
#> usethis                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 cli (>= 3.0.1), clipr (>= 0.3.0), crayon, curl (>= 2.7), desc\n(>= 1.4.0), fs (>= 1.3.0), gert (>= 1.4.1), gh (>= 1.2.1), glue\n(>= 1.3.0), jsonlite, lifecycle (>= 1.0.0), purrr, rappdirs,\nrlang (>= 1.0.0), rprojroot (>= 1.2), rstudioapi, stats, utils,\nwhisker, withr (>= 2.3.0), yaml
#> utf8                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> uuid                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> varSelRF                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> vcd                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  stats, utils, MASS, grDevices, colorspace, lmtest
#> vctrs                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           cli (>= 3.2.0), glue, rlang (>= 1.0.2)
#> VennDiagram                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    methods
#> VIM                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             car, grDevices, magrittr, robustbase, stats, sp,\nvcd,MASS,nnet,e1071,methods,Rcpp,utils,graphics,laeken,ranger,\ndata.table(>= 1.9.4)
#> viridis                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           stats, ggplot2 (>= 1.0.1), gridExtra
#> viridisLite                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> visdat                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             ggplot2, tidyr, dplyr, purrr, readr, magrittr, stats, tibble,\nglue
#> vroom                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            bit64, crayon, cli, glue, hms, lifecycle, methods, rlang (>=\n0.4.2), stats, tibble (>= 2.0.0), tzdb (>= 0.1.1), vctrs (>=\n0.2.0), tidyselect, withr
#> waiter                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                shiny, htmltools
#> waldo                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               cli, diffobj (>= 0.3.4), fansi, glue, methods, rematch2, rlang\n(>= 1.0.0), tibble
#> webshot                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      magrittr, jsonlite, callr
#> whisker                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           <NA>
#> withr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       graphics, grDevices, stats
#> xfun                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      stats, tools
#> xgboost                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Matrix (>= 1.1-0), methods, data.table (>= 1.9.6), jsonlite\n(>= 1.0),
#> xlsx                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 rJava, xlsxjars, grDevices, utils
#> xlsxjars                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> XML                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               <NA>
#> xml2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           methods
#> xopen                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         processx
#> xtable                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    stats, utils
#> xts                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            methods
#> XVector                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             methods, utils, tools, zlibbioc, BiocGenerics, S4Vectors,\nIRanges
#> yaml                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> yulab.utils                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      utils
#> zeallot                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           <NA>
#> zip                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               <NA>
#> zlibbioc                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> zoo                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   utils, graphics, grDevices, lattice (>= 0.20-27)
#> base                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> boot                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> class                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             MASS
#> cluster                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              graphics, grDevices, stats, utils
#> codetools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> compiler                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> datasets                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> foreign                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          methods, utils, stats
#> graphics                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     grDevices
#> grDevices                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> grid                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  grDevices, utils
#> KernSmooth                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        <NA>
#> lattice                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        grid, grDevices, graphics, stats, utils
#> MASS                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           methods
#> Matrix                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  methods, graphics, grid, stats, utils, lattice
#> methods                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   utils, stats
#> mgcv                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  methods, stats, graphics, Matrix, splines, utils
#> nlme                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   graphics, stats, utils, lattice
#> nnet                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> parallel                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               tools, compiler
#> rpart                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             <NA>
#> spatial                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           <NA>
#> splines                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                graphics, stats
#> stats                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       utils, grDevices, graphics
#> stats4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        graphics, methods, stats
#> survival                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              graphics, Matrix, methods, splines, stats, utils
#> tcltk                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            utils
#> tools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             <NA>
#> utils                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             <NA>
#>                                                                      LinkingTo
#> abind                                                                     <NA>
#> affy                                                            preprocessCore
#> affyio                                                                    <NA>
#> annotate                                                                  <NA>
#> AnnotationDbi                                                             <NA>
#> ape                                                                       Rcpp
#> aplot                                                                     <NA>
#> arm                                                                       <NA>
#> arules                                                                    <NA>
#> askpass                                                                   <NA>
#> assertthat                                                                <NA>
#> autokeras                                                                 <NA>
#> backports                                                                 <NA>
#> base64enc                                                                 <NA>
#> BBmisc                                                                    <NA>
#> BH                                                                        <NA>
#> Biobase                                                                   <NA>
#> BiocCheck                                                                 <NA>
#> BiocFileCache                                                             <NA>
#> BiocGenerics                                                              <NA>
#> BiocManager                                                               <NA>
#> Biocomb                                                                   Rcpp
#> BiocParallel                                                                BH
#> BiocStyle                                                                 <NA>
#> BiocVersion                                                               <NA>
#> biocViews                                                                 <NA>
#> biomaRt                                                                   <NA>
#> Biostrings                                         S4Vectors, IRanges, XVector
#> bit                                                                       <NA>
#> bit64                                                                     <NA>
#> bitops                                                                    <NA>
#> blob                                                                      <NA>
#> bookdown                                                                  <NA>
#> Boruta                                                                    <NA>
#> bounceR                                                                   <NA>
#> brew                                                                      <NA>
#> brio                                                                      <NA>
#> broom                                                                     <NA>
#> broom.helpers                                                             <NA>
#> bslib                                                                     <NA>
#> C50                                                                       <NA>
#> cachem                                                                    <NA>
#> calibrate                                                                 <NA>
#> callr                                                                     <NA>
#> car                                                                       <NA>
#> carData                                                                   <NA>
#> caret                                                                     <NA>
#> caTools                                                                   <NA>
#> cellranger                                                                <NA>
#> checkmate                                                                 <NA>
#> circlize                                                                  <NA>
#> classInt                                                                  <NA>
#> cli                                                                       <NA>
#> clipr                                                                     <NA>
#> clue                                                                      <NA>
#> clusterProfiler                                                           <NA>
#> coda                                                                      <NA>
#> coin                                                        libcoin (>= 1.0-9)
#> colorspace                                                                <NA>
#> combinat                                                                  <NA>
#> commonmark                                                                <NA>
#> ComplexHeatmap                                                            <NA>
#> config                                                                    <NA>
#> corrplot                                                                  <NA>
#> cowplot                                                                   <NA>
#> cpp11                                                                     <NA>
#> crayon                                                                    <NA>
#> credentials                                                               <NA>
#> crosstalk                                                                 <NA>
#> cubature                                                                  Rcpp
#> Cubist                                                                    <NA>
#> curl                                                                      <NA>
#> cutpointr                                                                 Rcpp
#> data.table                                                                <NA>
#> DBI                                                                       <NA>
#> dbplyr                                                                    <NA>
#> dbscan                                                                    Rcpp
#> deepnet                                                                   <NA>
#> DelayedArray                                                         S4Vectors
#> DEoptimR                                                                  <NA>
#> Deriv                                                                     <NA>
#> desc                                                                      <NA>
#> DESeq2                                                     Rcpp, RcppArmadillo
#> devtools                                                                  <NA>
#> DiceKriging                                                               <NA>
#> diffobj                                                                   <NA>
#> digest                                                                    <NA>
#> DMwR                                                                      <NA>
#> DO.db                                                                     <NA>
#> doParallel                                                                <NA>
#> DOSE                                                                      <NA>
#> downlit                                                                   <NA>
#> downloader                                                                <NA>
#> dplyr                                                                     <NA>
#> DT                                                                        <NA>
#> dtplyr                                                                    <NA>
#> e1071                                                                     <NA>
#> edgeR                                                                     Rcpp
#> ellipsis                                                                  <NA>
#> enrichplot                                                                <NA>
#> entropy                                                                   <NA>
#> epiDisplay                                                                <NA>
#> evaluate                                                                  <NA>
#> exactRankTests                                                            <NA>
#> fansi                                                                     <NA>
#> farver                                                                    <NA>
#> fastmap                                                                   <NA>
#> fastmatch                                                                 <NA>
#> feseR                                                                     <NA>
#> fgsea                                                                 Rcpp, BH
#> filelock                                                                  <NA>
#> fontawesome                                                               <NA>
#> forcats                                                                   <NA>
#> foreach                                                                   <NA>
#> formatR                                                                   <NA>
#> Formula                                                                   <NA>
#> fs                                                                        <NA>
#> FSelector                                                                 <NA>
#> funModeling                                                               <NA>
#> furrr                                                                     <NA>
#> futile.logger                                                             <NA>
#> futile.options                                                            <NA>
#> future                                                                    <NA>
#> future.apply                                                              <NA>
#> gargle                                                                    <NA>
#> gdata                                                                     <NA>
#> GDCRNATools                                                               <NA>
#> genefilter                                                                <NA>
#> geneplotter                                                               <NA>
#> generics                                                                  <NA>
#> GenomeInfoDb                                                              <NA>
#> GenomeInfoDbData                                                          <NA>
#> GenomicDataCommons                                                        <NA>
#> GenomicRanges                                               S4Vectors, IRanges
#> gert                                                                      <NA>
#> GetoptLong                                                                <NA>
#> ggbiplot                                                                  <NA>
#> ggforce                                                        Rcpp, RcppEigen
#> ggfun                                                                     <NA>
#> ggplot2                                                                   <NA>
#> ggplotify                                                                 <NA>
#> ggpubr                                                                    <NA>
#> ggraph                                                                    Rcpp
#> ggrepel                                                                   Rcpp
#> ggsci                                                                     <NA>
#> ggsignif                                                                  <NA>
#> ggtext                                                                    <NA>
#> ggtree                                                                    <NA>
#> gh                                                                        <NA>
#> gitcreds                                                                  <NA>
#> gld                                                                       <NA>
#> glmnet                                                         RcppEigen, Rcpp
#> GlobalOptions                                                             <NA>
#> globals                                                                   <NA>
#> glue                                                                      <NA>
#> gmodels                                                                   <NA>
#> GO.db                                                                     <NA>
#> googledrive                                                               <NA>
#> googlesheets4                                                             <NA>
#> GOSemSim                                                                  Rcpp
#> gower                                                                     <NA>
#> gplots                                                                    <NA>
#> graph                                                                     <NA>
#> graphlayouts                                               Rcpp, RcppArmadillo
#> gridExtra                                                                 <NA>
#> gridGraphics                                                              <NA>
#> gridtext                                                                  Rcpp
#> gt                                                                        <NA>
#> gtable                                                                    <NA>
#> gtools                                                                    <NA>
#> gtsummary                                                                 <NA>
#> hardhat                                                                   <NA>
#> hash                                                                      <NA>
#> haven                                                                    cpp11
#> here                                                                      <NA>
#> highr                                                                     <NA>
#> Hmisc                                                                     <NA>
#> hms                                                                       <NA>
#> htmlTable                                                                 <NA>
#> htmltools                                                                 <NA>
#> htmlwidgets                                                               <NA>
#> HTqPCR                                                                    <NA>
#> httpuv                                                             Rcpp, later
#> httr                                                                      <NA>
#> ids                                                                       <NA>
#> igraph                                                                    <NA>
#> imputeMissings                                                            <NA>
#> ini                                                                       <NA>
#> inum                                                                      <NA>
#> ipred                                                                     <NA>
#> IRanges                                                              S4Vectors
#> isoband                                                                   <NA>
#> iterators                                                                 <NA>
#> jpeg                                                                      <NA>
#> jquerylib                                                                 <NA>
#> jsonlite                                                                  <NA>
#> kableExtra                                                                <NA>
#> KEGGgraph                                                                 <NA>
#> KEGGREST                                                                  <NA>
#> keras                                                                     <NA>
#> kernlab                                                                   <NA>
#> klaR                                                                      <NA>
#> km.ci                                                                     <NA>
#> KMsurv                                                                    <NA>
#> knitr                                                                     <NA>
#> labeling                                                                  <NA>
#> labelled                                                                  <NA>
#> laeken                                                                    <NA>
#> lambda.r                                                                  <NA>
#> later                                                                     Rcpp
#> latticeExtra                                                              <NA>
#> lava                                                                      <NA>
#> lavaan                                                                    <NA>
#> lazyeval                                                                  <NA>
#> lhs                                                                       Rcpp
#> libcoin                                                                mvtnorm
#> lifecycle                                                                 <NA>
#> limma                                                                     <NA>
#> listenv                                                                   <NA>
#> lme4                                               Rcpp (>= 0.10.5), RcppEigen
#> lmom                                                                      <NA>
#> lmtest                                                                    <NA>
#> lobstr                                                                    Rcpp
#> locfit                                                                    <NA>
#> lubridate                                                     cpp11 (>= 0.2.7)
#> magick                                                                    Rcpp
#> magrittr                                                                  <NA>
#> maptools                                                                  <NA>
#> markdown                                                                  <NA>
#> MatchIt                                                     Rcpp, RcppProgress
#> MatrixGenerics                                                            <NA>
#> MatrixModels                                                              <NA>
#> matrixStats                                                               <NA>
#> maxstat                                                                   <NA>
#> mboost                                                                    <NA>
#> memoise                                                                   <NA>
#> mice                                                               cpp11, Rcpp
#> mime                                                                      <NA>
#> miniUI                                                                    <NA>
#> minqa                                                                     Rcpp
#> mitools                                                                   <NA>
#> mlbench                                                                   <NA>
#> mlr                                                                       <NA>
#> mnormt                                                                    <NA>
#> ModelMetrics                                                              Rcpp
#> modelr                                                                    <NA>
#> modeltools                                                                <NA>
#> moments                                                                   <NA>
#> mRMRe                                                                     <NA>
#> multcomp                                                                  <NA>
#> munsell                                                                   <NA>
#> mvtnorm                                                                   <NA>
#> My.stepwise                                                               <NA>
#> naniar                                                                    <NA>
#> networkD3                                                                 <NA>
#> nloptr                                                                testthat
#> nnls                                                                      <NA>
#> nondetects                                                                <NA>
#> norm                                                                      <NA>
#> np                                                                        <NA>
#> numDeriv                                                                  <NA>
#> OmicSelector                                                              <NA>
#> openssl                                                                   <NA>
#> org.Hs.eg.db                                                              <NA>
#> PairedData                                                                <NA>
#> pamr                                                                      <NA>
#> pander                                                                    Rcpp
#> parallelly                                                                <NA>
#> parallelMap                                                               <NA>
#> ParamHelpers                                                              <NA>
#> ParBayesianOptimization                                                   <NA>
#> parsetools                                                                <NA>
#> party                                                                  mvtnorm
#> partykit                                                                  <NA>
#> patchwork                                                                 <NA>
#> pathview                                                                  <NA>
#> pbivnorm                                                                  <NA>
#> pbkrtest                                                                  <NA>
#> pillar                                                                    <NA>
#> pkgbuild                                                                  <NA>
#> pkgcond                                                                   <NA>
#> pkgconfig                                                                 <NA>
#> pkgdown                                                                   <NA>
#> pkgload                                                                   <NA>
#> plogr                                                                     <NA>
#> plotly                                                                    <NA>
#> plyr                                                                      Rcpp
#> png                                                                       <NA>
#> polspline                                                                 <NA>
#> polyclip                                                                  <NA>
#> polynom                                                                   <NA>
#> postlogic                                                                 <NA>
#> praise                                                                    <NA>
#> preprocessCore                                                            <NA>
#> prettyunits                                                               <NA>
#> pROC                                                                      Rcpp
#> processx                                                                  <NA>
#> prodlim                                                                   Rcpp
#> profileR                                                                  <NA>
#> progress                                                                  <NA>
#> progressr                                                                 <NA>
#> promises                                                           later, Rcpp
#> proxy                                                                     <NA>
#> pryr                                                                      Rcpp
#> ps                                                                        <NA>
#> psych                                                                     <NA>
#> purrr                                                                     <NA>
#> purrrogress                                                               <NA>
#> quadprog                                                                  <NA>
#> quantmod                                                                  <NA>
#> quantreg                                                                  <NA>
#> questionr                                                                 <NA>
#> qvalue                                                                    <NA>
#> R.cache                                                                   <NA>
#> R.methodsS3                                                               <NA>
#> R.oo                                                                      <NA>
#> R.utils                                                                   <NA>
#> R6                                                                        <NA>
#> ragg                                                  systemfonts, textshaping
#> randomForest                                                              <NA>
#> ranger                                                         Rcpp, RcppEigen
#> RANN                                                                      <NA>
#> rappdirs                                                                  <NA>
#> rapportools                                                               <NA>
#> RBGL                                                                        BH
#> rcmdcheck                                                                 <NA>
#> RColorBrewer                                                              <NA>
#> Rcpp                                                                      <NA>
#> RcppArmadillo                                                             Rcpp
#> RcppEigen                                                                 Rcpp
#> RcppProgress                                                              <NA>
#> RcppTOML                                                                  Rcpp
#> RCurl                                                                     <NA>
#> readr                                                   cpp11, tzdb (>= 0.1.1)
#> readxl                                              cpp11 (>= 0.4.0), progress
#> recipes                                                                   <NA>
#> rematch                                                                   <NA>
#> rematch2                                                                  <NA>
#> remotes                                                                   <NA>
#> reprex                                                                    <NA>
#> resample                                                                  <NA>
#> reshape                                                                   <NA>
#> reshape2                                                                  Rcpp
#> reticulate                                                                Rcpp
#> rgl                                                                       <NA>
#> Rgraphviz                                                                 <NA>
#> rhandsontable                                                             <NA>
#> rJava                                                                     <NA>
#> rjson                                                                     <NA>
#> rlang                                                                     <NA>
#> rmarkdown                                                                 <NA>
#> rms                                                                       <NA>
#> robustbase                                                                <NA>
#> ROCR                                                                      <NA>
#> ROSE                                                                      <NA>
#> roxygen2                                                                 cpp11
#> rprojroot                                                                 <NA>
#> RSNNS                                                                     Rcpp
#> rsq                                                                       <NA>
#> RSQLite                                                 plogr (>= 0.2.0), Rcpp
#> rstatix                                                                   <NA>
#> rstudioapi                                                                <NA>
#> RUnit                                                                     <NA>
#> rversions                                                                 <NA>
#> rvest                                                                     <NA>
#> RWeka                                                                     <NA>
#> RWekajars                                                                 <NA>
#> S4Vectors                                                                 <NA>
#> sandwich                                                                  <NA>
#> sass                                                                      <NA>
#> scales                                                                    <NA>
#> scatterpie                                                                <NA>
#> selectr                                                                   <NA>
#> sessioninfo                                                               <NA>
#> shadowtext                                                                <NA>
#> shape                                                                     <NA>
#> shiny                                                                     <NA>
#> shinyfullscreen                                                           <NA>
#> shinyjqui                                                                 <NA>
#> shinyjs                                                                   <NA>
#> snow                                                                      <NA>
#> sourcetools                                                               <NA>
#> sp                                                                        <NA>
#> SparseM                                                                   <NA>
#> spFSR                                                                     <NA>
#> SQUAREM                                                                   <NA>
#> stabs                                                                     <NA>
#> stargazer                                                                 <NA>
#> stringdist                                                                <NA>
#> stringi                                                                   <NA>
#> stringr                                                                   <NA>
#> strucchange                                                               <NA>
#> styler                                                                    <NA>
#> SummarizedExperiment                                                      <NA>
#> summarytools                                                              <NA>
#> survey                                                                    <NA>
#> survminer                                                                 <NA>
#> survMisc                                                                  <NA>
#> sva                                                                       <NA>
#> svglite                                                     cpp11, systemfonts
#> sys                                                                       <NA>
#> systemfonts                                                   cpp11 (>= 0.2.1)
#> tableone                                                                  <NA>
#> TCGAbiolinks                                                              <NA>
#> TCGAbiolinksGUI.data                                                      <NA>
#> tensorflow                                                                <NA>
#> testextra                                                                 <NA>
#> testthat                                                                  <NA>
#> textshaping                           cpp11 (>= 0.2.1), systemfonts (>= 1.0.0)
#> tfautograph                                                               <NA>
#> tfruns                                                                    <NA>
#> TH.data                                                                   <NA>
#> tibble                                                                    <NA>
#> tictoc                                                                    <NA>
#> tidygraph                                                                cpp11
#> tidyr                                                         cpp11 (>= 0.4.0)
#> tidyselect                                                                <NA>
#> tidytemplate                                                              <NA>
#> tidytree                                                                  <NA>
#> tidyverse                                                                 <NA>
#> timeDate                                                                  <NA>
#> tinytex                                                                   <NA>
#> tmvnsim                                                                   <NA>
#> treeio                                                                    <NA>
#> TTR                                                                        xts
#> tweenr                                                                    Rcpp
#> tzdb                                                          cpp11 (>= 0.4.2)
#> UpSetR                                                                    <NA>
#> usethis                                                                   <NA>
#> utf8                                                                      <NA>
#> uuid                                                                      <NA>
#> varSelRF                                                                  <NA>
#> vcd                                                                       <NA>
#> vctrs                                                                     <NA>
#> VennDiagram                                                               <NA>
#> VIM                                                                       Rcpp
#> viridis                                                                   <NA>
#> viridisLite                                                               <NA>
#> visdat                                                                    <NA>
#> vroom                   progress (>= 1.2.1), cpp11 (>= 0.2.0), tzdb (>= 0.1.1)
#> waiter                                                                    <NA>
#> waldo                                                                     <NA>
#> webshot                                                                   <NA>
#> whisker                                                                   <NA>
#> withr                                                                     <NA>
#> xfun                                                                      <NA>
#> xgboost                                                                   <NA>
#> xlsx                                                                      <NA>
#> xlsxjars                                                                  <NA>
#> XML                                                                       <NA>
#> xml2                                                                      <NA>
#> xopen                                                                     <NA>
#> xtable                                                                    <NA>
#> xts                                                                        zoo
#> XVector                                                     S4Vectors, IRanges
#> yaml                                                                      <NA>
#> yulab.utils                                                               <NA>
#> zeallot                                                                   <NA>
#> zip                                                                       <NA>
#> zlibbioc                                                                  <NA>
#> zoo                                                                       <NA>
#> base                                                                      <NA>
#> boot                                                                      <NA>
#> class                                                                     <NA>
#> cluster                                                                   <NA>
#> codetools                                                                 <NA>
#> compiler                                                                  <NA>
#> datasets                                                                  <NA>
#> foreign                                                                   <NA>
#> graphics                                                                  <NA>
#> grDevices                                                                 <NA>
#> grid                                                                      <NA>
#> KernSmooth                                                                <NA>
#> lattice                                                                   <NA>
#> MASS                                                                      <NA>
#> Matrix                                                                    <NA>
#> methods                                                                   <NA>
#> mgcv                                                                      <NA>
#> nlme                                                                      <NA>
#> nnet                                                                      <NA>
#> parallel                                                                  <NA>
#> rpart                                                                     <NA>
#> spatial                                                                   <NA>
#> splines                                                                   <NA>
#> stats                                                                     <NA>
#> stats4                                                                    <NA>
#> survival                                                                  <NA>
#> tcltk                                                                     <NA>
#> tools                                                                     <NA>
#> utils                                                                     <NA>
#>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Suggests
#> abind                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> affy                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  tkWidgets (>= 1.19.0), affydata, widgetTools
#> affyio                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        <NA>
#> annotate                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges,\nrae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db,\norg.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit,
#> AnnotationDbi                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit,\nTxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db,\nAnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr
#> ape                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    gee, expm, igraph, phangorn
#> aplot                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ggtree
#> arm                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           <NA>
#> arules                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   pmml, XML, arulesViz, arulesCBA, testthat
#> askpass                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   testthat
#> assertthat                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          testthat, covr
#> autokeras                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           testthat, covr
#> backports                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     <NA>
#> base64enc                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     <NA>
#> BBmisc                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         testthat, microbenchmark, codetools
#> BH                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            <NA>
#> Biobase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   tools, tkWidgets, ALL, RUnit, golubEsets
#> BiocCheck                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  RUnit, BiocGenerics, Biobase, jsonlite, rmarkdown,\ndownloader, devtools (>= 1.4.1), usethis, BiocStyle
#> BiocFileCache                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   testthat, knitr, BiocStyle, rmarkdown, rtracklayer
#> BiocGenerics                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Biobase, S4Vectors, IRanges, GenomicRanges, DelayedArray,\nBiostrings, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2,\nflowClust, MSnbase, annotate, RUnit
#> BiocManager                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          BiocVersion, remotes, rmarkdown, testthat, withr, curl, knitr
#> Biocomb                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> BiocParallel                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel,\nRmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14,\nTxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,\nRsamtools, GenomicAlignments, ShortRead, codetools, RUnit,\nBiocStyle, knitr, batchtools, data.table
#> BiocStyle                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           BiocGenerics, RUnit, htmltools
#> BiocVersion                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   <NA>
#> biocViews                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          BiocGenerics, knitr, commonmark
#> biomaRt                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             BiocStyle, knitr, rmarkdown, testthat, mockery
#> Biostrings                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>=\n1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),\nBSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe,\nhgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy\n(>= 1.41.3), affydata (>= 1.11.5), RUnit
#> bit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             testthat (>= 0.11.0), roxygen2, knitr, rmarkdown,\nmicrobenchmark, bit64 (>= 4.0.0), ff (>= 4.0.0)
#> bit64                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> bitops                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        <NA>
#> blob                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     covr, crayon, pillar (>= 1.2.1), testthat
#> bookdown                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    bslib (>= 0.2.4), downlit (>= 0.4.0), htmlwidgets, jsonlite,\nrstudioapi, miniUI, rsconnect (>= 0.4.3), servr (>= 0.13),\nshiny, tibble, testit (>= 0.9), tufte, xml2, webshot, testthat\n(>= 3.1.0), withr (>= 2.3.0)
#> Boruta                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  mlbench, rFerns, randomForest, testthat, xgboost, survival
#> bounceR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> brew                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      testthat
#> brio                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     covr, testthat (>= 2.1.0)
#> broom                                                                                                                                                                                                                                                                                                                                                   AER, akima, AUC, bbmle, betareg, biglm, binGroup, boot,\nbtergm (>= 1.10.6), car, caret, cluster, cmprsk, coda, covr,\ndrc, e1071, emmeans, epiR, ergm (>= 3.10.4), fixest (>= 0.9.0),\ngam (>= 1.15), gee, geepack, glmnet, glmnetUtils, gmm, Hmisc,\nirlba, joineRML, Kendall, knitr, ks, Lahman, lavaan, leaps,\nlfe, lm.beta, lme4, lmodel2, lmtest (>= 0.9.38), lsmeans, maps,\nmaptools, margins, MASS, Matrix, mclust, mediation, metafor,\nmfx, mgcv, mlogit, modeldata, modeltests, muhaz, multcomp,\nnetwork, nnet, orcutt (>= 2.2), ordinal, plm, poLCA, psych,\nquantreg, rgeos, rmarkdown, robust, robustbase, rsample,\nsandwich, sp, spdep (>= 1.1), spatialreg, speedglm, spelling,\nsurvey, survival, systemfit, testthat (>= 2.1.0), tseries,\nvars, zoo
#> broom.helpers                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          brms (>= 2.13.0), broom.mixed, cmprsk, covr, datasets,\nemmeans, forcats, gam, gee, geepack, ggplot2, glmmTMB, glue,\ngt, gtsummary, knitr, lavaan, lfe, lme4 (>= 1.1.28), MASS,\nmgcv, mice, nnet, ordinal, parameters, plm, rmarkdown,\nrstanarm, spelling, survey, survival, testthat, tidycmprsk,\nVGAM
#> bslib                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            shiny (>= 1.6.0), rmarkdown (>= 2.7), thematic, knitr,\ntestthat, withr, rappdirs, curl, magrittr
#> C50                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              covr, knitr, modeldata, rmarkdown
#> cachem                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    testthat
#> calibrate                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     <NA>
#> callr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              cli, covr, ps, rprojroot, spelling, testthat, withr (>=\n2.3.0)
#> car                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          alr4, boot, coxme, effects, knitr, leaps, lmtest, Matrix,\nMatrixModels, rgl (>= 0.93.960), rio, sandwich, SparseM,\nsurvival, survey
#> carData                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             car (>= 3.0-0)
#> caret                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   BradleyTerry2, covr, Cubist, dplyr, earth (>= 2.2-3),\nellipse, fastICA, gam (>= 1.15), ipred, kernlab, klaR, knitr,\nMASS, Matrix, mda, mgcv, mlbench, MLmetrics, nnet, pamr, party\n(>= 0.9-99992), pls, proxy, randomForest, RANN, rmarkdown,\nrpart, spls, subselect, superpc, testthat (>= 0.9.1), themis\n(>= 0.1.3)
#> caTools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                MASS, rpart
#> cellranger                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             covr, testthat (>= 1.0.0), knitr, rmarkdown
#> checkmate                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  R6, fastmatch, data.table (>= 1.9.8), devtools, ggplot2,\nknitr, magrittr, microbenchmark, rmarkdown, testthat (>=\n3.0.4), tinytest (>= 1.1.0), tibble
#> circlize                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                knitr, dendextend (>= 1.0.1), ComplexHeatmap (>= 2.0.0),\ngridBase, png, markdown, bezier, covr, rmarkdown
#> classInt                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              spData (>= 0.2.6.2), units, knitr, rmarkdown
#> cli                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              asciicast, callr, covr, digest, grDevices, htmltools,\nhtmlwidgets, knitr, methods, mockery, processx, ps (>=\n1.3.4.9000), rlang, rmarkdown, rstudioapi, shiny, testthat,\ntibble, whoami, withr
#> clipr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            covr, knitr, rmarkdown, rstudioapi (>= 0.5), testthat (>=\n2.0.0)
#> clue                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     e1071, lpSolve (>= 5.5.7), quadprog (>= 1.4-8), relations
#> clusterProfiler                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    AnnotationHub, knitr, rmarkdown, org.Hs.eg.db, prettydoc,\nReactomePA, testthat
#> coda                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> coin                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        xtable, e1071, vcd, TH.data (>= 1.0-7)
#> colorspace                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   datasets, utils, KernSmooth, MASS, kernlab, mvtnorm, vcd,\ntcltk, shiny, shinyjs, ggplot2, dplyr, scales, grid, png, jpeg,\nknitr, rmarkdown, RColorBrewer, rcartocolor, scico, viridis,\nwesanderson
#> combinat                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> commonmark                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    curl, testthat, xml2
#> ComplexHeatmap                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff,\nfastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport,\ngrImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12),\ngridGraphics, gplots, rmarkdown, Cairo
#> config                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  testthat, knitr, rmarkdown, covr, spelling
#> corrplot                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 seriation, knitr, RColorBrewer, rmarkdown, magrittr,\nprettydoc, testthat
#> cowplot                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Cairo, covr, dplyr, forcats, gridGraphics (>= 0.4-0), knitr,\nlattice, magick, maps, PASWR, patchwork, rmarkdown, ragg,\ntestthat (>= 1.0.0), tidyr, vdiffr (>= 0.3.0), VennDiagram
#> cpp11                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                bench, brio, callr, cli, covr, decor, desc, ggplot2, glue,\nknitr, lobstr, mockery, progress, rmarkdown, scales, Rcpp,\ntestthat, tibble, utils, vctrs, withr
#> crayon                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        mockery, rstudioapi, testthat, withr
#> credentials                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             testthat, knitr, rmarkdown
#> crosstalk                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         shiny, ggplot2, testthat (>= 2.1.0), sass, bslib
#> cubature                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               testthat, knitr, mvtnorm, benchr, rmarkdown
#> Cubist                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   mlbench, knitr, modeldata, dplyr (>= 0.7.4), rlang,\ntidyrules, rmarkdown
#> curl                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             spelling, testthat (>= 1.0.0), knitr, jsonlite, rmarkdown,\nmagrittr, httpuv (>= 1.4.4), webutils
#> cutpointr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              KernSmooth (>= 2.23-15), fANCOVA (>= 0.5-1), testthat (>=\n1.0.2), doRNG (>= 1.6), doParallel (>= 1.0.11), knitr,\nrmarkdown, mgcv (>= 1.8), crayon (>= 1.3.4), registry (>=\n0.5-1), pkgmaker(>= 0.31.1), vctrs (>= 0.2.4)
#> data.table                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 bit64 (>= 4.0.0), bit (>= 4.0.4), curl, R.utils, xts,\nnanotime, zoo (>= 1.8-1), yaml, knitr, rmarkdown
#> DBI                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  blob, covr, DBItest, dbplyr, downlit, dplyr, glue, hms,\nknitr, magrittr, RMariaDB, rmarkdown, rprojroot, RSQLite (>=\n1.1-2), testthat, xml2
#> dbplyr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         bit64, covr, knitr, Lahman, nycflights13, odbc, RMariaDB (>=\n1.0.2), rmarkdown, RPostgres (>= 1.1.3), RPostgreSQL, RSQLite\n(>= 2.1.0), testthat (>= 3.0.2), tidyr
#> dbscan                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        fpc, microbenchmark, testthat, dendextend, igraph, knitr,\nrmarkdown
#> deepnet                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> DelayedArray                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      BiocParallel, HDF5Array (>= 1.17.12), genefilter,\nSummarizedExperiment, airway, lobstr, DelayedMatrixStats,\nknitr, rmarkdown, BiocStyle, RUnit
#> DEoptimR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> Deriv                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     testthat
#> desc                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            callr, covr, gh, spelling, testthat, whoami, withr
#> DESeq2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer,\napeglm, ashr, tximport, tximeta, tximportData, readr, pbapply,\nairway, pasilla (>= 0.2.10), glmGamPoi, BiocManager
#> devtools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           BiocManager (>= 1.30.12), covr (>= 3.5.1), curl (>= 4.3),\ndigest (>= 0.6.27), DT (>= 0.17), foghorn (>= 1.3.2), gh (>=\n1.2.1), gmailr (>= 1.0.0), knitr (>= 1.31), lintr (>= 2.0.1),\nMASS, mockery (>= 0.4.2), pingr (>= 2.0.1), pkgdown (>= 1.6.1),\nrhub (>= 1.1.1), rmarkdown (>= 2.7), spelling (>= 2.2)
#> DiceKriging                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          rgenoud (>= 5.8-2.0), foreach, doParallel, testthat, numDeriv
#> diffobj                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           knitr, rmarkdown
#> digest                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   tinytest, simplermarkdown
#> DMwR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> DO.db                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> doParallel                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            caret, mlbench, rpart, RUnit
#> DOSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         prettydoc, clusterProfiler, knitr, rmarkdown, org.Hs.eg.db,\ntestthat
#> downlit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   covr, htmltools, jsonlite, leaflet, MASS, pkgload, rmarkdown,\ntestthat (>= 3.0.0), xml2
#> downloader                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                testthat
#> dplyr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        bench, broom, callr, covr, DBI, dbplyr (>= 1.4.3), ggplot2,\nknitr, Lahman, lobstr, microbenchmark, nycflights13, purrr,\nrmarkdown, RMySQL, RPostgreSQL, RSQLite, testthat (>= 3.1.1),\ntidyr, withr
#> DT                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        knitr (>= 1.8), rmarkdown, shiny (>= 1.6), bslib, testit
#> dtplyr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       bench, covr, knitr, rmarkdown, testthat (>= 3.0.0), tidyr (>=\n1.1.0)
#> e1071                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            cluster, mlbench, nnet, randomForest, rpart, SparseM, xtable,\nMatrix, MASS, slam
#> edgeR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 jsonlite, readr, rhdf5, splines, Biobase, AnnotationDbi,\nSummarizedExperiment, org.Hs.eg.db
#> ellipsis                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            covr, testthat
#> enrichplot                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               clusterProfiler, dplyr, europepmc, ggupset, knitr, rmarkdown,\norg.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, AnnotationDbi,\nggplotify, ggridges, grDevices, gridExtra, ggnewscale, ggrepel\n(>= 0.9.0), ggstar, treeio, scales, tidytree, rlang,\nggtreeExtra, tidydr
#> entropy                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
#> epiDisplay                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
#> evaluate                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          covr, ggplot2, lattice, testthat
#> exactRankTests                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            survival
#> fansi                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   unitizer, knitr, rmarkdown
#> farver                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   testthat (>= 2.1.0), covr
#> fastmap                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        testthat (>= 2.1.1)
#> fastmatch                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     <NA>
#> feseR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   testthat, knitr, rmarkdown
#> fgsea                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             testthat, knitr, rmarkdown, reactome.db, AnnotationDbi,\nparallel, org.Mm.eg.db, limma, GEOquery
#> filelock                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          callr (>= 2.0.0), covr, testthat
#> fontawesome                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            covr, knitr, testthat, rsvg
#> forcats                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    covr, dplyr, ggplot2, knitr, readr, rmarkdown, testthat
#> foreach                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 randomForest, doMC, doParallel, testthat, knitr, rmarkdown
#> formatR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                rstudioapi, shiny, testit, rmarkdown, knitr
#> Formula                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> fs                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              testthat, covr, pillar (>= 1.0.0), tibble (>= 1.1.0), crayon,\nrmarkdown, knitr, withr, spelling, vctrs (>= 0.3.0)
#> FSelector                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           mlbench, rpart
#> funModeling                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       knitr, rmarkdown
#> furrr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     carrier, covr, dplyr (>= 0.7.4), knitr, listenv (>= 0.6.0),\nmagrittr, rmarkdown, testthat (>= 3.0.0), tidyselect, withr
#> futile.logger                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   testthat, jsonlite
#> futile.options                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                <NA>
#> future                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       methods, RhpcBLASctl, R.rsp, markdown
#> future.apply                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           datasets, stats, tools, listenv (>= 0.8.0), R.rsp, markdown
#> gargle                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               aws.ec2metadata, aws.signature, covr, httpuv, knitr, mockr,\nrmarkdown, sodium, spelling, testthat (>= 3.0.0)
#> gdata                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        RUnit
#> GDCRNATools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             knitr, testthat, rmarkdown
#> genefilter                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer,\nBiocStyle, knitr
#> geneplotter                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db
#> generics                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         covr, pkgload, testthat (>= 3.0.0), tibble, withr
#> GenomeInfoDb                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures,\nTxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome,\nBSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2,\nBSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr
#> GenomeInfoDbData                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <NA>
#> GenomicDataCommons                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              BiocStyle, knitr, rmarkdown, DT, testthat, listviewer,\nggplot2, GenomicAlignments, Rsamtools, BiocParallel,\nTxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation, maftools,\nR.utils, data.table
#> GenomicRanges                                                                                                                                                                                                                                                                                                                                                                                                                                                           Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>=\n2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>=\n1.13.53), GenomicAlignments, rtracklayer, BSgenome,\nGenomicFeatures, Gviz, VariantAnnotation, AnnotationHub,\nDESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14,\npasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe,\nBSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19,\nBSgenome.Mmusculus.UCSC.mm10,\nTxDb.Athaliana.BioMart.plantsmart22,\nTxDb.Dmelanogaster.UCSC.dm3.ensGene,\nTxDb.Hsapiens.UCSC.hg19.knownGene,\nTxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr,\nrmarkdown, BiocStyle
#> gert                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          spelling, knitr, rmarkdown, testthat
#> GetoptLong                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         testthat (>= 1.0.0), knitr, markdown, rmarkdown
#> ggbiplot                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> ggforce                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         sessioninfo, concaveman, deldir, reshape2, units (>= 0.4-6),\ncovr
#> ggfun                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ggplotify, knitr, rmarkdown, prettydoc
#> ggplot2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              covr, ragg, dplyr, ggplot2movies, hexbin, Hmisc, interp,\nknitr, lattice, mapproj, maps, maptools, multcomp, munsell,\nnlme, profvis, quantreg, RColorBrewer, rgeos, rmarkdown, rpart,\nsf (>= 0.7-3), svglite (>= 1.2.0.9001), testthat (>= 2.1.0),\nvdiffr (>= 1.0.0), xml2
#> ggplotify                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   aplot, colorspace, cowplot, ggimage, knitr, rmarkdown,\nlattice, prettydoc, vcd, utils
#> ggpubr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      grDevices, knitr, RColorBrewer, gtable
#> ggraph                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               network, knitr, rmarkdown, purrr, tibble, seriation, deldir,\ngganimate, covr
#> ggrepel                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   knitr, rmarkdown, testthat, gridExtra, devtools, prettydoc,\nggbeeswarm, dplyr, magrittr, readr, stringr
#> ggsci                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        knitr, rmarkdown, gridExtra, reshape2
#> ggsignif                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   knitr, rmarkdown, spelling, testthat, vdiffr (>= 1.0.2)
#> ggtext                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    cowplot, dplyr, glue, knitr, rmarkdown, testthat, vdiffr
#> ggtree                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr,\nprettydoc, rmarkdown, stats, testthat, tibble, glue
#> gh                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               covr, knitr, mockery, rmarkdown, rprojroot, spelling,\ntestthat (>= 2.3.2), withr
#> gitcreds                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         codetools, testthat, knitr, mockery, oskeyring, rmarkdown,\nwithr
#> gld                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
#> glmnet                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      knitr, lars, testthat, xfun, rmarkdown
#> GlobalOptions                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     testthat (>= 1.0.0), knitr, markdown, GetoptLong
#> globals                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> glue                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  covr, crayon, DBI, dplyr, forcats, ggplot2, knitr, magrittr,\nmicrobenchmark, R.utils, rmarkdown, rprintf, RSQLite, stringr,\ntestthat (>= 3.0.0), vctrs (>= 0.3.0), waldo (>= 0.3.0), withr
#> gmodels                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         gplots, gtools, Matrix, nlme, lme4 (>= 0.999999-0)
#> GO.db                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          DBI
#> googledrive                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       covr, curl, downlit, dplyr (>= 1.0.0), knitr, mockr,\nrmarkdown, roxygen2, sodium, spelling, testthat (>= 3.0.0)
#> googlesheets4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                covr, readr, rmarkdown, sodium, spelling, testthat (>=\n3.0.0), withr
#> GOSemSim                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr,\nrmarkdown, org.Hs.eg.db, prettydoc, testthat, ROCR
#> gower                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         tinytest (>= 0.9.3),
#> gplots                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     grid, MASS, knitr, r2d2
#> graph                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SparseM (>= 0.36), XML, RBGL, RUnit, cluster
#> graphlayouts                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               oaqc, testthat, ggraph, ggplot2, knitr, rmarkdown, uwot
#> gridExtra                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   ggplot2, egg, lattice, knitr, testthat
#> gridGraphics                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    magick (>= 1.3), pdftools (>= 1.6)
#> gridtext                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  covr, knitr, rmarkdown, testthat, vdiffr
#> gt                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            covr, knitr, paletteer, testthat (>= 2.1.0), RColorBrewer,\nlubridate, rmarkdown, rvest, shiny, tidyr, webshot, xml2
#> gtable                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          covr, testthat, knitr, rmarkdown, ggplot2, profvis
#> gtools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 car, gplots, knitr, rstudioapi, SGP, taxize
#> gtsummary                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            aod (>= 1.3.1), broom.mixed (>= 0.2.7), car (>= 3.0-11),\ncovr, effectsize (>= 0.6.0), emmeans (>= 1.7.3), flextable (>=\n0.6.10), ftExtra (>= 0.4.0), geepack, GGally (>= 2.1.0), Hmisc,\nhuxtable (>= 5.4.0), insight (>= 0.15.0), kableExtra (>=\n1.3.4), lme4, mgcv, mice (>= 3.10.0), nnet, officer, openxlsx,\nparameters (>= 0.16.0), parsnip (>= 0.1.7), rmarkdown, sandwich\n(>= 3.0.1), scales, smd (>= 0.6.6), spelling (>= 2.2), survey,\nsurvival (>= 3.2-11), testthat (>= 3.0.4), tidycmprsk (>=\n0.1.2), workflows (>= 0.2.4)
#> hardhat                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              covr, crayon, devtools, knitr, Matrix, modeldata (>= 0.0.2),\nrecipes (>= 0.1.8), rmarkdown (>= 2.3), roxygen2, testthat (>=\n2.1.0), usethis
#> hash                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      testthat
#> haven                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  covr, crayon, fs, knitr, pillar (>= 1.4.0), rmarkdown,\ntestthat (>= 3.0.0)
#> here                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            conflicted, covr, fs, knitr, palmerpenguins, plyr, readr,\nrlang, rmarkdown, testthat, uuid, withr
#> highr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      knitr, markdown, testit
#> Hmisc                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              acepack, chron, rms, mice, tables, knitr, plotly (>= 4.5.6),\nrlang, plyr, VGAM
#> hms                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      crayon, lubridate, pillar (>= 1.1.0), testthat (>= 3.0.0)
#> htmlTable                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           testthat, XML, xml2, Hmisc, reshape, rmarkdown, chron,\nlubridate, tibble, purrr, tidyselect, glue, rlang, tidyr (>=\n0.7.2), dplyr (>= 0.7.4)
#> htmltools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            markdown, testthat, withr, Cairo, ragg, shiny
#> htmlwidgets                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    knitr (>= 1.8), rmarkdown, testthat
#> HTqPCR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     statmod
#> httpuv                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            testthat, callr, curl, websocket
#> httr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  covr, httpuv, jpeg, knitr, png, readr, rmarkdown, testthat\n(>= 0.8.0), xml2
#> ids                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           knitr, rcorpora, rmarkdown, testthat
#> igraph                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                ape, graph, igraphdata, rgl, scales, stats4, tcltk, testthat,\nwithr, digest
#> imputeMissings                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                <NA>
#> ini                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       testthat
#> inum                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> ipred                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               mvtnorm, mlbench, TH.data, randomForest, party
#> IRanges                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    XVector, GenomicRanges, Rsamtools, GenomicAlignments,\nGenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset,\nRUnit, BiocStyle
#> isoband                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               covr, ggplot2, knitr, magick, microbenchmark, rmarkdown, sf,\ntestthat, xml2
#> iterators                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           RUnit, foreach
#> jpeg                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> jquerylib                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 testthat
#> jsonlite                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  httr, curl, vctrs, testthat, knitr, rmarkdown, R.rsp, sf
#> kableExtra                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                testthat, magick, formattable, sparkline
#> KEGGgraph                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db,\nSPIA
#> KEGGREST                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      RUnit, BiocGenerics, knitr, markdown
#> keras                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         ggplot2, testthat (>= 2.1.0), knitr, rmarkdown, callr,\ntfdatasets, withr, png, jpeg
#> kernlab                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> klaR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         scatterplot3d (>= 0.3-22), som, mlbench, rpart, e1071
#> km.ci                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> KMsurv                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        <NA>
#> knitr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     markdown, formatR, testit, digest, rgl (>= 0.95.1201),\ncodetools, rmarkdown, htmlwidgets (>= 0.7), webshot, tikzDevice\n(>= 0.10), tinytex, reticulate (>= 1.4), JuliaCall (>= 0.11.1),\nmagick, png, jpeg, gifski, xml2 (>= 1.2.0), httr, DBI (>=\n0.4-1), showtext, tibble, sass, bslib, ragg, styler (>= 1.2.0),\ntargets (>= 0.6.0)
#> labeling                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> labelled                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   testthat, knitr, rmarkdown, questionr, snakecase, utf8, covr,\nspelling
#> laeken                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        <NA>
#> lambda.r                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    testit
#> later                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        knitr, rmarkdown, testthat (>= 2.1.0)
#> latticeExtra                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             maps, mapproj, deldir, tripack, quantreg, zoo, MASS, mgcv
#> lava                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      KernSmooth, Matrix, Rgraphviz, data.table, ellipse, fields,\ngeepack, gof (>= 0.9), graph, knitr, bookdown, rmarkdown,\nigraph (>= 0.6), lava.tobit (>= 0.4.7), lavaSearch2, lme4,\nmagrittr, mets (>= 1.1), nlme, optimx, polycor, quantreg, rgl,\nR.rsp (>= 0.40), testthat (>= 0.11), visNetwork, zoo
#> lavaan                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        <NA>
#> lazyeval                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              knitr, rmarkdown (>= 0.2.65), testthat, covr
#> lhs                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               testthat, assertthat, DoE.base, knitr, rmarkdown
#> libcoin                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       coin
#> lifecycle                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             covr, crayon, lintr, tidyverse, knitr, rmarkdown, testthat\n(>= 3.0.1), tools, tibble, vctrs
#> limma                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db,\ngplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines,\nstatmod (>= 1.2.2), vsn
#> listenv                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   R.utils, R.rsp, markdown
#> lme4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        knitr, rmarkdown, PKPDmodels, MEMSS, testthat (>= 0.8.1),\nggplot2, mlmRev, optimx (>= 2013.8.6), gamm4, pbkrtest, HSAUR3,\nnumDeriv, car, dfoptim, mgcv, statmod, rr2, semEff, tibble
#> lmom                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> lmtest                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    car, strucchange, sandwich, dynlm, stats4, survival, AER
#> lobstr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             covr, pillar, pkgdown, testthat
#> locfit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 interp, gam
#> lubridate                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            covr, knitr, testthat (>= 2.1.0), vctrs (>= 0.3.0), rmarkdown
#> magick                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               av (>= 0.3), spelling, jsonlite, methods, knitr, rmarkdown,\nrsvg, webp, pdftools, ggplot2, gapminder, IRdisplay, tesseract\n(>= 2.0), gifski
#> magrittr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   covr, knitr, rlang, rmarkdown, testthat
#> maptools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    rgeos (>= 0.1-8), spatstat.geom (>= 1.65-0), PBSmapping,\nmaps, RColorBrewer, raster, polyclip, plotrix, spatstat.linnet\n(>= 1.65-3), spatstat.utils (>= 1.19.0), spatstat (>= 2.0-0)
#> markdown                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              knitr, RCurl
#> MatchIt                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      optmatch (>= 0.10.0), Matching, rgenoud, nnet, rpart, mgcv,\nCBPS (>= 0.17), dbarts, randomForest (>= 4.7-1), glmnet (>=\n4.0), gbm (>= 2.1.7), cobalt (>= 4.2.3), boot, lmtest, sandwich\n(>= 2.5-1), survival, RcppProgress (>= 0.4.2), Rglpk,\nRsymphony, gurobi, knitr, rmarkdown
#> MatrixGenerics                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   sparseMatrixStats, DelayedMatrixStats, SummarizedExperiment,\ntestthat (>= 2.1.0)
#> MatrixModels                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  <NA>
#> matrixStats                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 base64enc, ggplot2, knitr, markdown, microbenchmark,\nR.devices, R.rsp
#> maxstat                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          TH.data, survival
#> mboost                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           TH.data, MASS, fields, BayesX, gbm, mlbench, RColorBrewer,\nrpart (>= 4.0-3), randomForest, nnet, testthat (>= 0.10.0),\nkangar00
#> memoise                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    digest, aws.s3, covr, googleAuthR, googleCloudStorageR, httr,\ntestthat
#> mice                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               broom.mixed, decor, glmnet, haven, knitr, lme4, lmtest, MASS,\nmetafor, mitml, miceadds, nnet, pan, randomForest, ranger,\nrmarkdown, rpart, survival, testthat
#> mime                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> miniUI                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        <NA>
#> minqa                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> mitools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             RODBC, foreign
#> mlbench                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    lattice
#> mlr                     ada, adabag, bartMachine, batchtools, bit64, brnn, bst, C50,\ncare, caret (>= 6.0-57), class, clue, cluster, ClusterR,\nclusterSim (>= 0.44-5), cmaes, cowplot, crs, Cubist, deepnet,\nDiceKriging, DiscriMiner, e1071, earth, elasticnet, emoa,\nevtree, extraTrees, fda.usc, FDboost, FNN, forecast (>= 8.3),\nfpc, frbs, FSelector, FSelectorRcpp (>= 0.3.5), gbm, GenSA,\nggpubr, glmnet, GPfit, h2o (>= 3.6.0.8), Hmisc, irace (>= 2.0),\nkernlab, kknn, klaR, knitr, laGP, LiblineaR, lintr (>=\n1.0.0.9001), MASS, mboost, mco, mda, memoise, mlbench, mldr,\nmlrMBO, mmpf, modeltools, mRMRe, neuralnet, nnet, nodeHarvest\n(>= 0.7-3), numDeriv, pamr, pander, party, pec, penalized (>=\n0.9-47), pls, PMCMRplus, praznik (>= 5.0.0), randomForest,\nrandomForestSRC (>= 2.7.0), ranger (>= 0.8.0), rappdirs,\nrefund, rex, rFerns, rgenoud, rknn, rmarkdown, Rmpi, ROCR,\nrotationForest, rpart, RRF, rrlda, rsm, RSNNS, rucrdtw, RWeka,\nsda, sf, smoof, snow, sparseLDA, stepPlr, survAUC, svglite,\nSwarmSVM, testthat, tgp, TH.data, tidyr, tsfeatures, vdiffr,\nwavelets, xgboost (>= 0.7)
#> mnormt                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        <NA>
#> ModelMetrics                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              testthat
#> modelr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           compiler, covr, ggplot2, testthat
#> modeltools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    <NA>
#> moments                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> mRMRe                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> multcomp                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        lme4 (>= 0.999375-16), nlme, robustbase, coin, MASS, foreign,\nxtable, lmtest, coxme (>= 2.2-1), SimComp, ISwR, tram (>=\n0.2-5), fixest (>= 0.10)
#> munsell                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          ggplot2, testthat
#> mvtnorm                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> My.stepwise                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   <NA>
#> naniar                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       knitr, rmarkdown, testthat (>= 2.1.0), rpart, rpart.plot,\ncovr, gridExtra, wakefield, vdiffr, here, simputation,\nimputeTS, gdtools, Hmisc, spelling
#> networkD3                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          htmltools (>= 0.2.6), jsonlite,
#> nloptr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           knitr, rmarkdown, xml2, testthat (>= 3.0.0), covr
#> nnls                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> nondetects                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 knitr, rmarkdown, BiocStyle (>= 1.0.0), RUnit, BiocGenerics\n(>= 0.8.0)
#> norm                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> np                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            MASS
#> numDeriv                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> OmicSelector                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      knitr, rmarkdown
#> openssl                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               curl, testthat (>= 2.1.0), digest, knitr, rmarkdown,\njsonlite, jose, sodium
#> org.Hs.eg.db                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  DBI, annotate, RUnit
#> PairedData                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    <NA>
#> pamr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> pander                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   grid, lattice, ggplot2 (>= 0.9.2), sylly, sylly.en, logger,\nsurvival, microbenchmark, zoo, nlme, descr, MASS, knitr,\nrmarkdown, tables, reshape, memisc, Epi, randomForest, tseries,\ngtable, rms, forecast, data.table
#> parallelly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    <NA>
#> parallelMap                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    BatchJobs (>= 1.8), batchtools (>= 0.9.6), data.table, Rmpi,\nrpart, snow, testthat
#> ParamHelpers                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              akima, covr, eaf, emoa, GGally, ggplot2, grid, gridExtra,\nirace (>= 2.1), lhs, plyr, reshape2, testthat
#> ParBayesianOptimization                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            knitr, rmarkdown, xgboost, doParallel, testthat
#> parsetools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        covr, knitr, rmarkdown, testthat
#> party                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             TH.data (>= 1.0-3), mlbench, colorspace, MASS, vcd, ipred,\nvarImp, randomForest
#> partykit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             XML, pmml, rJava, sandwich, strucchange, vcd, AER, mlbench,\nTH.data (>= 1.0-3), coin (>= 1.1-0), RWeka (>= 0.4-19),\ndatasets, parallel, psychotools (>= 0.3-0), psychotree, party\n(>= 1.3-0), randomForest
#> patchwork                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 knitr, rmarkdown, gridGraphics, gridExtra, ragg, testthat (>=\n2.1.0), vdiffr, covr, png
#> pathview                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   gage, org.Mm.eg.db, RUnit, BiocGenerics
#> pbivnorm                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> pbkrtest                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> pillar                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    bit64, debugme, DiagrammeR, dplyr, formattable, ggplot2,\nknitr, lubridate, nanotime, nycflights13, palmerpenguins,\nrmarkdown, scales, stringi, survival, testthat (>= 3.1.1),\ntibble, units (>= 0.7.2), vdiffr, withr
#> pkgbuild                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Rcpp, cpp11, testthat, covr
#> pkgcond                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             covr, testthat
#> pkgconfig                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   covr, testthat, disposables (>= 1.0.3)
#> pkgdown                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             covr, diffviewer, evaluate, htmltools, htmlwidgets, knitr,\nlifecycle, methods, openssl, pkgload (>= 1.0.2), rsconnect,\nrstudioapi, rticles, sass, testthat (>= 3.1.3), tools
#> pkgload                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     bitops, covr, pkgbuild, Rcpp, testthat
#> plogr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Rcpp
#> plotly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 MASS, maps, hexbin, ggthemes, GGally, testthat, knitr,\ndevtools, shiny (>= 1.1.0), shinytest (>= 1.3.0), curl,\nrmarkdown, Cairo, broom, webshot, listviewer, dendextend,\nmaptools, rgeos, sf, png, IRdisplay, processx, plotlyGeoAssets,\nforcats, palmerpenguins, rversions, reticulate
#> plyr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      abind, covr, doParallel, foreach, iterators, itertools,\ntcltk, testthat
#> png                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           <NA>
#> polspline                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     <NA>
#> polyclip                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> polynom                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           knitr, rmarkdown
#> postlogic                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           testthat, covr
#> praise                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    testthat
#> preprocessCore                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                <NA>
#> prettyunits                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              codetools, covr, testthat
#> pROC                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               microbenchmark, tcltk, MASS, logcondens, doParallel,\ntestthat, vdiffr, ggplot2
#> processx                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   callr (>= 3.7.0), cli (>= 1.1.0), codetools, covr, curl,\ndebugme, parallel, testthat (>= 3.0.0), withr
#> prodlim                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> profileR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> progress                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Rcpp, testthat, withr
#> progressr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      graphics, tcltk, beepr, crayon, pbmcapply, progress, purrr,\nforeach, plyr, doFuture, future, future.apply, furrr,\nrstudioapi, shiny, commonmark, base64enc, tools
#> promises                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             testthat, future (>= 1.21.0), fastmap (>= 1.1.0), purrr,\nknitr, rmarkdown, vembedr, spelling
#> proxy                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          cba
#> pryr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           testthat (>= 0.8.0)
#> ps                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          callr, covr, curl, pingr, processx (>= 3.1.0), R6, rlang,\ntestthat (>= 3.0.0), tibble
#> psych                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       psychTools, GPArotation, lavaan, lme4, Rcsdp, graph, knitr,\nRgraphviz
#> purrr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              covr, crayon, dplyr (>= 0.7.8), knitr, rmarkdown, testthat,\ntibble, tidyselect
#> purrrogress                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              covr, datasets, stringi, testthat, tibble
#> quadprog                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> quantmod                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           DBI,RMySQL,RSQLite,timeSeries,xml2,downloader,jsonlite(>=\n1.1)
#> quantreg                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    tripack, akima, rgl, logspline, nor1mix, Formula, zoo, R.rsp,\nconquer
#> questionr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            testthat, roxygen2, dplyr, ggplot2, tidyr, janitor, forcats,\nknitr, rmarkdown, survey, Hmisc
#> qvalue                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       knitr
#> R.cache                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> R.methodsS3                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              codetools
#> R.oo                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         tools
#> R.utils                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         digest (>= 0.6.10)
#> R6                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  testthat, pryr
#> ragg                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                covr, testthat, grid, graphics
#> randomForest                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    RColorBrewer, MASS
#> ranger                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    covr, survival, testthat
#> RANN                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      testthat
#> rappdirs                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                roxygen2, testthat (>= 3.0.0), covr, withr
#> rapportools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   <NA>
#> RBGL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Rgraphviz, XML, RUnit, BiocGenerics
#> rcmdcheck                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              covr, knitr, mockery, processx, ps, rmarkdown, svglite,\ntestthat, webfakes
#> RColorBrewer                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  <NA>
#> Rcpp                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            tinytest, inline, rbenchmark, pkgKitten (>= 0.1.2)
#> RcppArmadillo                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             tinytest, Matrix (>= 1.3.0), pkgKitten, reticulate, slam
#> RcppEigen                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              inline, tinytest, pkgKitten, microbenchmark
#> RcppProgress                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           RcppArmadillo, devtools, roxygen2, testthat
#> RcppTOML                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  tinytest
#> RCurl                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          XML
#> readr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         covr, curl, datasets, knitr, rmarkdown, spelling, stringi,\ntestthat (>= 3.1.2), tzdb (>= 0.1.1), waldo, withr, xml2
#> readxl                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       knitr, rmarkdown, testthat (>= 3.0.0)
#> recipes                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        covr, ddalpha, dials (>= 0.0.10.9001), ggplot2, igraph,\nkernlab, knitr, modeldata, parsnip (>= 0.1.7), RANN, RcppRoll,\nrmarkdown, rpart, rsample, RSpectra, testthat (>= 3.0.0),\nworkflows, xml2
#> rematch                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             covr, testthat
#> rematch2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            covr, testthat
#> remotes                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       brew, callr, codetools, curl, covr, git2r (>= 0.23.0), knitr,\nmockery, pkgbuild (>= 1.0.1), pingr, rmarkdown, rprojroot,\ntestthat, webfakes, withr
#> reprex                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             covr, fortunes, miniUI, mockr, rprojroot, sessioninfo, shiny,\nspelling, styler (>= 1.2.0), testthat (>= 3.0.2)
#> resample                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   splus2R
#> reshape                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> reshape2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        covr, lattice, testthat (>= 0.8.0)
#> reticulate                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                callr, knitr, rlang, rmarkdown, testthat
#> rgl                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  MASS, rmarkdown, deldir (>= 1.0-4), orientlib, lattice,\nmisc3d, magick, plotrix (>= 3.7-3), tripack, interp,\nalphashape3d, tcltk, js (>= 1.2), akima, webshot2, downlit (>=\n0.4.0), pkgdown, extrafont, shiny, manipulateWidget (>= 0.9.0),\ntestthat, markdown, crosstalk
#> Rgraphviz                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 RUnit, BiocGenerics, XML
#> rhandsontable                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                knitr, rmarkdown, shiny (>= 0.13), miniUI (>= 0.1.1),\nrstudioapi (>= 0.6), htmltools
#> rJava                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> rjson                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> rlang                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  cli (>= 3.1.0), covr, crayon, fs, glue, knitr, magrittr,\nmethods, pillar, rmarkdown, stats, testthat (>= 3.0.0), tibble,\nusethis, vctrs (>= 0.2.3), withr
#> rmarkdown                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  digest, dygraphs, fs, rsconnect, downlit (>= 0.4.0), katex\n(>= 1.4.0), sass (>= 0.4.0), shiny (>= 1.6.0), testthat (>=\n3.0.3), tibble, tufte, vctrs, withr (>= 2.4.2)
#> rms                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  boot, tcltk, plotly (>= 4.5.6), knitr, mice, rmsb, nnet, VGAM
#> robustbase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    grid, MASS, lattice, boot, cluster, Matrix, robust,\nfit.models, MPV, xtable, ggplot2, GGally, RColorBrewer,\nreshape2, sfsmisc, catdata, doParallel, foreach, skewt
#> ROCR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    testthat, knitr, rmarkdown
#> ROSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       MASS, nnet, rpart, tree
#> roxygen2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  covr, R.methodsS3, R.oo, rmarkdown, testthat (>= 3.1.2),
#> rprojroot                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    covr, knitr, lifecycle, mockr, rmarkdown, testthat (>=\n3.0.0), withr
#> RSNNS                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 scatterplot3d,NeuralNetTools
#> rsq                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
#> RSQLite                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         callr, DBItest (>= 1.7.0), gert, gh, knitr, rmarkdown, hms,\nrvest, testthat, xml2
#> rstatix                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               knitr, rmarkdown, ggpubr, graphics, emmeans, coin, boot,\ntestthat, spelling
#> rstudioapi                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       testthat, knitr, rmarkdown, clipr
#> RUnit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               XML (>= 3.1.0)
#> rversions                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        mockery, testthat
#> rvest                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               covr, glue, knitr, readr, rmarkdown, repurrrsive, spelling,\nstringi (>= 0.3.1), testthat (>= 3.0.2), webfakes
#> RWeka                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          partykit (>= 0.8.0), mlbench, e1071
#> RWekajars                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     <NA>
#> S4Vectors                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      IRanges, GenomicRanges, SummarizedExperiment, Matrix,\nDelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle
#> sandwich                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         AER, car, geepack, lattice, lmtest, MASS, multiwayvcov,\nparallel, pcse, plm, pscl, scatterplot3d, stats4, strucchange,\nsurvival
#> sass                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                testthat, knitr, rmarkdown, withr, shiny, curl
#> scales                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            bit64, covr, dichromat, ggplot2, hms (>= 0.5.0), stringi,\ntestthat (>= 3.0.0), waldo (>= 0.4.0)
#> scatterpie                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       knitr, rmarkdown, prettydoc, maps
#> selectr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        testthat, XML, xml2
#> sessioninfo                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           callr, covr, mockery, reticulate, rmarkdown, testthat, withr
#> shadowtext                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             knitr, rmarkdown, prettydoc
#> shape                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> shiny                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     datasets, Cairo (>= 1.5-5), testthat (>= 3.0.0), knitr (>=\n1.6), markdown, rmarkdown, ggplot2, reactlog (>= 1.0.0),\nmagrittr, shinytest (>= 1.4.0.9003), yaml, future, dygraphs,\nragg, showtext, sass
#> shinyfullscreen                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 testthat, spelling
#> shinyjqui                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 ggplot2, highcharter, knitr, markdown, rmarkdown, plotly
#> shinyjs                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           htmltools (>= 0.2.9), knitr (>= 1.7), rmarkdown, shinyAce,\nshinydisconnect, testthat (>= 0.9.1)
#> snow                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      rlecuyer
#> sourcetools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               testthat
#> sp                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   RColorBrewer, rgdal (>= 1.2-3), rgeos (>= 0.3-13), gstat,\nmaptools, deldir, knitr, rmarkdown
#> SparseM                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> spFSR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              caret (>= 6.0), MASS (>= 7.3), knitr, rmarkdown
#> SQUAREM                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     setRNG
#> stabs                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            glmnet, lars, mboost (> 2.3-0), gamboostLSS (>= 1.2-0),\nTH.data, hdi, testthat, knitr, rmarkdown
#> stargazer                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     <NA>
#> stringdist                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                tinytest
#> stringi                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> stringr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   covr, htmltools, htmlwidgets, knitr, rmarkdown, testthat
#> strucchange                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           stats4, car, dynlm, e1071, foreach, lmtest, mvtnorm, tseries
#> styler                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                data.tree (>= 0.1.6), digest, dplyr, here, knitr, prettycode,\nrmarkdown, roxygen2, rstudioapi (>= 0.7), testthat (>= 2.1.0)
#> SummarizedExperiment                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  HDF5Array (>= 1.7.5), annotate, AnnotationDbi, hgu95av2.db,\nGenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, jsonlite,\nrhdf5, airway (>= 1.15.1), BiocStyle, knitr, rmarkdown, RUnit,\ntestthat, digest
#> summarytools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 forcats, formatR, kableExtra, knitr, magrittr, rmarkdown,\nrstudioapi
#> survey                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     foreign, MASS, KernSmooth, hexbin, RSQLite, quantreg,\nparallel, CompQuadForm, DBI, AER
#> survminer                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   knitr, flexsurv, cmprsk, markdown, testthat, rmarkdown
#> survMisc                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> sva                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat
#> svglite                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       htmltools, testthat, xml2 (>= 1.0.0), covr, fontquiver (>=\n0.2.0), knitr, rmarkdown
#> sys                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              unix (>= 1.4), spelling, testthat
#> systemfonts                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     testthat (>= 2.1.0), covr, knitr, rmarkdown, tools
#> tableone                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       survival, testthat, Matrix, Matching, reshape2, ggplot2,\nknitr, geepack, lme4, lmerTest, rmarkdown
#> TCGAbiolinks                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           jpeg, png, BiocStyle, rmarkdown, devtools, maftools,\nparmigene, c3net, minet, dnet, Biobase, affy, testthat, sesame,\nAnnotationHub, ExperimentHub, pathview, clusterProfiler,\nSeurat, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph,\nsupraHex, limma, edgeR, sva, EDASeq, survminer, genefilter,\ngridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3),\nscales, grid
#> TCGAbiolinksGUI.data                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        BiocStyle, knitr, rmarkdown, readr, DT
#> tensorflow                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       testthat (>= 2.1.0), keras, callr
#> testextra                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            covr, devtools, withr, rstudioapi, htmltools, shiny, yaml, DT
#> testthat                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              covr, curl (>= 0.9.5), diffviewer (>= 0.1.0), knitr, mockery,\nrmarkdown, rstudioapi, shiny, usethis, vctrs (>= 0.1.0), xml2
#> textshaping                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 covr, knitr, rmarkdown
#> tfautograph                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 rlang, tensorflow, testthat (>= 2.1.0)
#> tfruns                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     testthat, knitr, withr, here, rmarkdown
#> TH.data                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      dplyr, gdata, plyr, trtf, tram, rms, coin, ATR, multcomp,\ngridExtra, vcd, colorspace, lattice, knitr
#> tibble                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                bench, bit64, blob, brio, callr, cli, covr, crayon (>=\n1.3.4), DiagrammeR, dplyr, evaluate, formattable, ggplot2, hms,\nhtmltools, knitr, lubridate, mockr, nycflights13, pkgbuild,\npkgload, purrr, rmarkdown, stringi, testthat (>= 3.0.2), tidyr,\nwithr
#> tictoc                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        <NA>
#> tidygraph                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       network, data.tree, ape, graph, methods, testthat, covr,\nseriation, netrankr, influenceR, NetSwan
#> tidyr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            covr, data.table, jsonlite, knitr, readr, repurrrsive (>=\n1.0.0), rmarkdown, testthat (>= 3.0.0)
#> tidyselect                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         covr, crayon, dplyr, knitr, magrittr, rmarkdown, testthat (>=\n3.1.1), tibble (>= 2.1.3), withr
#> tidytemplate                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      knitr, rmarkdown
#> tidytree                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              knitr, rmarkdown, prettydoc, testthat, utils
#> tidyverse                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          covr, feather, glue, knitr, rmarkdown, testthat
#> timeDate                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               date, RUnit
#> tinytex                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         testit, rstudioapi
#> tmvnsim                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> treeio                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Biostrings, ggplot2, ggtree, igraph, knitr, rmarkdown,\nphangorn, prettydoc, testthat, tidyr, vroom, xml2, yaml
#> TTR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          RUnit
#> tweenr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              testthat, covr
#> tzdb                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     covr, testthat (>= 3.0.0)
#> UpSetR                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       knitr
#> usethis                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           covr, knitr, magick, mockr, pkgload, rmarkdown, roxygen2 (>=\n7.1.2), spelling (>= 1.2), styler (>= 1.2.0), testthat (>=\n3.1.0)
#> utf8                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               cli, covr, knitr, rlang, rmarkdown, testthat (>= 3.0.0),\nwithr
#> uuid                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> varSelRF                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> vcd                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     KernSmooth, mvtnorm, kernlab, HSAUR3, coin
#> vctrs                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  bit64, covr, crayon, dplyr (>= 0.8.5), generics, knitr,\npillar (>= 1.4.4), pkgdown (>= 2.0.1), rmarkdown, testthat (>=\n3.0.0), tibble (>= 3.1.3), withr, xml2, waldo (>= 0.2.0),\nzeallot
#> VennDiagram                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               testthat
#> VIM                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        dplyr, testthat (>= 2.1.0), knitr, rmarkdown, reactable
#> viridis                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     hexbin (>= 1.27.0), scales, MASS, knitr, dichromat,\ncolorspace, raster, rasterVis, httr, mapproj, vdiffr, svglite\n(>= 1.2.0), testthat, covr, rmarkdown, rgdal, maps
#> viridisLite                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 hexbin (>= 1.27.0), ggplot2 (>= 1.0.1), testthat, covr
#> visdat                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   testthat, plotly (>= 4.5.6), knitr, rmarkdown, vdiffr,\ngdtools, spelling
#> vroom                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         archive, bench (>= 1.1.0), covr, curl, dplyr, forcats, fs,\nggplot2, knitr, patchwork, prettyunits, purrr, rmarkdown,\nrstudioapi, scales, spelling, testthat (>= 2.1.0), tidyr,\nutils, waldo, xml2
#> waiter                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          R6, httr, knitr, packer, rmarkdown
#> waldo                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   covr, R6, testthat (>= 3.0.0), withr, xml2
#> webshot                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            httpuv, knitr, rmarkdown, shiny
#> whisker                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   markdown
#> withr                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         callr, covr, DBI, knitr, lattice, methods, rlang, rmarkdown\n(>= 2.12), RSQLite, testthat (>= 3.0.0)
#> xfun                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           testit, parallel, codetools, rstudioapi, tinytex (>= 0.30),\nmime, markdown, knitr, htmltools, remotes, pak, rhub, renv,\ncurl, jsonlite, rmarkdown
#> xgboost                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          knitr, rmarkdown, ggplot2 (>= 1.0.1), DiagrammeR (>= 0.9.0),\nCkmeans.1d.dp (>= 3.3.1), vcd (>= 1.3), testthat, lintr, igraph\n(>= 1.0.1), float, crayon, titanic
#> xlsx                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           rprojroot, testthat, covr, tibble, knitr, rmarkdown
#> xlsxjars                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> XML                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  bitops, RCurl
#> xml2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   covr, curl, httr, knitr, magrittr, mockery, rmarkdown,\ntestthat (>= 2.1.0)
#> xopen                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 ps, testthat
#> xtable                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   knitr, plm, zoo, survival
#> xts                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          timeSeries, timeDate, tseries, chron, fts, tis, RUnit
#> XVector                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Biostrings, drosophila2probe, RUnit
#> yaml                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         RUnit
#> yulab.utils                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               pkgbuild
#> zeallot                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                testthat, knitr, rmarkdown, purrr, magrittr
#> zip                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            covr, processx, R6, testthat, withr
#> zlibbioc                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> zoo                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   AER, coda, chron, fts, ggplot2 (>= 3.0.0), mondate, scales,\nstinepack, strucchange, timeDate, timeSeries, tis, tseries, xts
#> base                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       methods
#> boot                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                MASS, survival
#> class                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> cluster                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               MASS, Matrix
#> codetools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     <NA>
#> compiler                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> datasets                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> foreign                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <NA>
#> graphics                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> grDevices                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               KernSmooth
#> grid                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          <NA>
#> KernSmooth                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           MASS, carData
#> lattice                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             KernSmooth, MASS, latticeExtra
#> MASS                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 lattice, nlme, nnet, survival
#> Matrix                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  expm, MASS
#> methods                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  codetools
#> mgcv                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      parallel, survival, MASS
#> nlme                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Hmisc, MASS, SASmixed
#> nnet                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          MASS
#> parallel                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   methods
#> rpart                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     survival
#> spatial                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       MASS
#> splines                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Matrix, methods
#> stats                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     MASS, Matrix, SuppDists, methods, stats4
#> stats4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        <NA>
#> survival                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <NA>
#> tcltk                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         <NA>
#> tools                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            codetools, methods, xml2, curl, commonmark, knitr, xfun, mathjaxr
#> utils                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             methods, xml2, commonmark, knitr
#>                                                                                                                                                                                                                                                               Enhances
#> abind                                                                                                                                                                                                                                                             <NA>
#> affy                                                                                                                                                                                                                                                              <NA>
#> affyio                                                                                                                                                                                                                                                            <NA>
#> annotate                                                                                                                                                                                                                                                          <NA>
#> AnnotationDbi                                                                                                                                                                                                                                                     <NA>
#> ape                                                                                                                                                                                                                                                               <NA>
#> aplot                                                                                                                                                                                                                                                             <NA>
#> arm                                                                                                                                                                                                                                                               <NA>
#> arules                                                                                                                                                                                                                                                            <NA>
#> askpass                                                                                                                                                                                                                                                           <NA>
#> assertthat                                                                                                                                                                                                                                                        <NA>
#> autokeras                                                                                                                                                                                                                                                         <NA>
#> backports                                                                                                                                                                                                                                                         <NA>
#> base64enc                                                                                                                                                                                                                                                          png
#> BBmisc                                                                                                                                                                                                                                                            <NA>
#> BH                                                                                                                                                                                                                                                                <NA>
#> Biobase                                                                                                                                                                                                                                                           <NA>
#> BiocCheck                                                                                                                                                                                                                                                codetoolsBioC
#> BiocFileCache                                                                                                                                                                                                                                                     <NA>
#> BiocGenerics                                                                                                                                                                                                                                                      <NA>
#> BiocManager                                                                                                                                                                                                                                                       <NA>
#> Biocomb                                                                                                                                                                                                                                                           <NA>
#> BiocParallel                                                                                                                                                                                                                                                      <NA>
#> BiocStyle                                                                                                                                                                                                                                                         <NA>
#> BiocVersion                                                                                                                                                                                                                                                       <NA>
#> biocViews                                                                                                                                                                                                                                                         <NA>
#> biomaRt                                                                                                                                                                                                                                                           <NA>
#> Biostrings                                                                                                                                                                                                                                                        Rmpi
#> bit                                                                                                                                                                                                                                                               <NA>
#> bit64                                                                                                                                                                                                                                                             <NA>
#> bitops                                                                                                                                                                                                                                                            <NA>
#> blob                                                                                                                                                                                                                                                              <NA>
#> bookdown                                                                                                                                                                                                                                                          <NA>
#> Boruta                                                                                                                                                                                                                                                            <NA>
#> bounceR                                                                                                                                                                                                                                                           <NA>
#> brew                                                                                                                                                                                                                                                              <NA>
#> brio                                                                                                                                                                                                                                                              <NA>
#> broom                                                                                                                                                                                                                                                             <NA>
#> broom.helpers                                                                                                                                                                                                                                                     <NA>
#> bslib                                                                                                                                                                                                                                                             <NA>
#> C50                                                                                                                                                                                                                                                               <NA>
#> cachem                                                                                                                                                                                                                                                            <NA>
#> calibrate                                                                                                                                                                                                                                                         <NA>
#> callr                                                                                                                                                                                                                                                             <NA>
#> car                                                                                                                                                                                                                                                               <NA>
#> carData                                                                                                                                                                                                                                                           <NA>
#> caret                                                                                                                                                                                                                                                             <NA>
#> caTools                                                                                                                                                                                                                                                           <NA>
#> cellranger                                                                                                                                                                                                                                                        <NA>
#> checkmate                                                                                                                                                                                                                                                         <NA>
#> circlize                                                                                                                                                                                                                                                          <NA>
#> classInt                                                                                                                                                                                                                                                          <NA>
#> cli                                                                                                                                                                                                                                                               <NA>
#> clipr                                                                                                                                                                                                                                                             <NA>
#> clue                                                                                                                                                                                  RWeka, ape, cba, cclust, flexclust, flexmix, kernlab, mclust,\nmovMF, modeltools
#> clusterProfiler                                                                                                                                                                                                                                                   <NA>
#> coda                                                                                                                                                                                                                                                              <NA>
#> coin                                                                                                                                                                                                                                                              <NA>
#> colorspace                                                                                                                                                                                                                                                        <NA>
#> combinat                                                                                                                                                                                                                                                          <NA>
#> commonmark                                                                                                                                                                                                                                                        <NA>
#> ComplexHeatmap                                                                                                                                                                                                                                                    <NA>
#> config                                                                                                                                                                                                                                                            <NA>
#> corrplot                                                                                                                                                                                                                                                          <NA>
#> cowplot                                                                                                                                                                                                                                                           <NA>
#> cpp11                                                                                                                                                                                                                                                             <NA>
#> crayon                                                                                                                                                                                                                                                            <NA>
#> credentials                                                                                                                                                                                                                                                       <NA>
#> crosstalk                                                                                                                                                                                                                                                         <NA>
#> cubature                                                                                                                                                                                                                                                          <NA>
#> Cubist                                                                                                                                                                                                                                                            <NA>
#> curl                                                                                                                                                                                                                                                              <NA>
#> cutpointr                                                                                                                                                                                                                                                         <NA>
#> data.table                                                                                                                                                                                                                                                        <NA>
#> DBI                                                                                                                                                                                                                                                               <NA>
#> dbplyr                                                                                                                                                                                                                                                            <NA>
#> dbscan                                                                                                                                                                                                                                                            <NA>
#> deepnet                                                                                                                                                                                                                                                           <NA>
#> DelayedArray                                                                                                                                                                                                                                                      <NA>
#> DEoptimR                                                                                                                                                                                                                                                    robustbase
#> Deriv                                                                                                                                                                                                                                                             <NA>
#> desc                                                                                                                                                                                                                                                              <NA>
#> DESeq2                                                                                                                                                                                                                                                            <NA>
#> devtools                                                                                                                                                                                                                                                          <NA>
#> DiceKriging                                                                                                                                                                                                                                                       <NA>
#> diffobj                                                                                                                                                                                                                                                           <NA>
#> digest                                                                                                                                                                                                                                                            <NA>
#> DMwR                                                                                                                                                                                                                                                              <NA>
#> DO.db                                                                                                                                                                                                                                                             <NA>
#> doParallel                                                                                                                                                                                                                                                    compiler
#> DOSE                                                                                                                                                                                                                                                              <NA>
#> downlit                                                                                                                                                                                                                                                           <NA>
#> downloader                                                                                                                                                                                                                                                        <NA>
#> dplyr                                                                                                                                                                                                                                                             <NA>
#> DT                                                                                                                                                                                                                                                                <NA>
#> dtplyr                                                                                                                                                                                                                                                            <NA>
#> e1071                                                                                                                                                                                                                                                             <NA>
#> edgeR                                                                                                                                                                                                                                                             <NA>
#> ellipsis                                                                                                                                                                                                                                                          <NA>
#> enrichplot                                                                                                                                                                                                                                                        <NA>
#> entropy                                                                                                                                                                                                                                                           <NA>
#> epiDisplay                                                                                                                                                                                                                                                        <NA>
#> evaluate                                                                                                                                                                                                                                                          <NA>
#> exactRankTests                                                                                                                                                                                                                                                    <NA>
#> fansi                                                                                                                                                                                                                                                             <NA>
#> farver                                                                                                                                                                                                                                                            <NA>
#> fastmap                                                                                                                                                                                                                                                           <NA>
#> fastmatch                                                                                                                                                                                                                                                         <NA>
#> feseR                                                                                                                                                                                                                                                             <NA>
#> fgsea                                                                                                                                                                                                                                                             <NA>
#> filelock                                                                                                                                                                                                                                                          <NA>
#> fontawesome                                                                                                                                                                                                                                                       <NA>
#> forcats                                                                                                                                                                                                                                                           <NA>
#> foreach                                                                                                                                                                                                                                                           <NA>
#> formatR                                                                                                                                                                                                                                                           <NA>
#> Formula                                                                                                                                                                                                                                                           <NA>
#> fs                                                                                                                                                                                                                                                                <NA>
#> FSelector                                                                                                                                                                                                                                                         <NA>
#> funModeling                                                                                                                                                                                                                                                       <NA>
#> furrr                                                                                                                                                                                                                                                             <NA>
#> futile.logger                                                                                                                                                                                                                                                     <NA>
#> futile.options                                                                                                                                                                                                                                                    <NA>
#> future                                                                                                                                                                                                                                                            <NA>
#> future.apply                                                                                                                                                                                                                                                      <NA>
#> gargle                                                                                                                                                                                                                                                            <NA>
#> gdata                                                                                                                                                                                                                                                             <NA>
#> GDCRNATools                                                                                                                                                                                                                                                       <NA>
#> genefilter                                                                                                                                                                                                                                                        <NA>
#> geneplotter                                                                                                                                                                                                                                                       <NA>
#> generics                                                                                                                                                                                                                                                          <NA>
#> GenomeInfoDb                                                                                                                                                                                                                                                      <NA>
#> GenomeInfoDbData                                                                                                                                                                                                                                                  <NA>
#> GenomicDataCommons                                                                                                                                                                                                                                                <NA>
#> GenomicRanges                                                                                                                                                                                                                                                     <NA>
#> gert                                                                                                                                                                                                                                                              <NA>
#> GetoptLong                                                                                                                                                                                                                                                        <NA>
#> ggbiplot                                                                                                                                                                                                                                                          <NA>
#> ggforce                                                                                                                                                                                                                                                           <NA>
#> ggfun                                                                                                                                                                                                                                                             <NA>
#> ggplot2                                                                                                                                                                                                                                                             sp
#> ggplotify                                                                                                                                                                                                                                                         <NA>
#> ggpubr                                                                                                                                                                                                                                                            <NA>
#> ggraph                                                                                                                                                                                                                                                            <NA>
#> ggrepel                                                                                                                                                                                                                                                           <NA>
#> ggsci                                                                                                                                                                                                                                                             <NA>
#> ggsignif                                                                                                                                                                                                                                                          <NA>
#> ggtext                                                                                                                                                                                                                                                            <NA>
#> ggtree                                                                                                                                                                                                                                                            <NA>
#> gh                                                                                                                                                                                                                                                                <NA>
#> gitcreds                                                                                                                                                                                                                                                          <NA>
#> gld                                                                                                                                                                                                                                                               <NA>
#> glmnet                                                                                                                                                                                                                                                            <NA>
#> GlobalOptions                                                                                                                                                                                                                                                     <NA>
#> globals                                                                                                                                                                                                                                                           <NA>
#> glue                                                                                                                                                                                                                                                              <NA>
#> gmodels                                                                                                                                                                                                                                                           <NA>
#> GO.db                                                                                                                                                                                                                                                             <NA>
#> googledrive                                                                                                                                                                                                                                                       <NA>
#> googlesheets4                                                                                                                                                                                                                                                     <NA>
#> GOSemSim                                                                                                                                                                                                                                                          <NA>
#> gower                                                                                                                                                                                                                                                             <NA>
#> gplots                                                                                                                                                                                                                                                            <NA>
#> graph                                                                                                                                                                                                                                                        Rgraphviz
#> graphlayouts                                                                                                                                                                                                                                                      <NA>
#> gridExtra                                                                                                                                                                                                                                                         <NA>
#> gridGraphics                                                                                                                                                                                                                                                      <NA>
#> gridtext                                                                                                                                                                                                                                                          <NA>
#> gt                                                                                                                                                                                                                                                                <NA>
#> gtable                                                                                                                                                                                                                                                            <NA>
#> gtools                                                                                                                                                                                                                                                            <NA>
#> gtsummary                                                                                                                                                                                                                                                         <NA>
#> hardhat                                                                                                                                                                                                                                                           <NA>
#> hash                                                                                                                                                                                                                                                              <NA>
#> haven                                                                                                                                                                                                                                                             <NA>
#> here                                                                                                                                                                                                                                                              <NA>
#> highr                                                                                                                                                                                                                                                             <NA>
#> Hmisc                                                                                                                                                                                                                                                             <NA>
#> hms                                                                                                                                                                                                                                                               <NA>
#> htmlTable                                                                                                                                                                                                                                                         <NA>
#> htmltools                                                                                                                                                                                                                                                        knitr
#> htmlwidgets                                                                                                                                                                                                                                             shiny (>= 1.1)
#> HTqPCR                                                                                                                                                                                                                                                            <NA>
#> httpuv                                                                                                                                                                                                                                                            <NA>
#> httr                                                                                                                                                                                                                                                              <NA>
#> ids                                                                                                                                                                                                                                                               <NA>
#> igraph                                                                                                                                                                                                                                                            <NA>
#> imputeMissings                                                                                                                                                                                                                                                    <NA>
#> ini                                                                                                                                                                                                                                                               <NA>
#> inum                                                                                                                                                                                                                                                              <NA>
#> ipred                                                                                                                                                                                                                                                             <NA>
#> IRanges                                                                                                                                                                                                                                                           <NA>
#> isoband                                                                                                                                                                                                                                                           <NA>
#> iterators                                                                                                                                                                                                                                                         <NA>
#> jpeg                                                                                                                                                                                                                                                              <NA>
#> jquerylib                                                                                                                                                                                                                                                         <NA>
#> jsonlite                                                                                                                                                                                                                                                          <NA>
#> kableExtra                                                                                                                                                                                                                                                        <NA>
#> KEGGgraph                                                                                                                                                                                                                                                         <NA>
#> KEGGREST                                                                                                                                                                                                                                                          <NA>
#> keras                                                                                                                                                                                                                                                             <NA>
#> kernlab                                                                                                                                                                                                                                                           <NA>
#> klaR                                                                                                                                                                                                                            clustMixType, randomForest, ClustVarLV
#> km.ci                                                                                                                                                                                                                                                             <NA>
#> KMsurv                                                                                                                                                                                                                                                            <NA>
#> knitr                                                                                                                                                                                                                                                             <NA>
#> labeling                                                                                                                                                                                                                                                          <NA>
#> labelled                                                                                                                                                                                                                                                        memisc
#> laeken                                                                                                                                                                                                                                                            <NA>
#> lambda.r                                                                                                                                                                                                                                                          <NA>
#> later                                                                                                                                                                                                                                                             <NA>
#> latticeExtra                                                                                                                                                                                                                                                      <NA>
#> lava                                                                                                                                                                                                                                                              <NA>
#> lavaan                                                                                                                                                                                                                                                            <NA>
#> lazyeval                                                                                                                                                                                                                                                          <NA>
#> lhs                                                                                                                                                                                                                                                               <NA>
#> libcoin                                                                                                                                                                                                                                                           <NA>
#> lifecycle                                                                                                                                                                                                                                                         <NA>
#> limma                                                                                                                                                                                                                                                             <NA>
#> listenv                                                                                                                                                                                                                                                           <NA>
#> lme4                                                                                                                                                                                                                                                              <NA>
#> lmom                                                                                                                                                                                                                                                              <NA>
#> lmtest                                                                                                                                                                                                                                                            <NA>
#> lobstr                                                                                                                                                                                                                                                            <NA>
#> locfit                                                                                                                                                                                                                                                            <NA>
#> lubridate                                                                                                                                                                                                                                    chron, timeDate, tis, zoo
#> magick                                                                                                                                                                                                                                                            <NA>
#> magrittr                                                                                                                                                                                                                                                          <NA>
#> maptools                                                                                                                                                                                                                                                        gpclib
#> markdown                                                                                                                                                                                                                                                          <NA>
#> MatchIt                                                                                                                                                                                                                                                           <NA>
#> MatrixGenerics                                                                                                                                                                                                                                                    <NA>
#> MatrixModels                                                                                                                                                                                                                                                      <NA>
#> matrixStats                                                                                                                                                                                                                                                       <NA>
#> maxstat                                                                                                                                                                                                                                                           <NA>
#> mboost                                                                                                                                                                                                                                                            <NA>
#> memoise                                                                                                                                                                                                                                                           <NA>
#> mice                                                                                                                                                                                                                                                              <NA>
#> mime                                                                                                                                                                                                                                                              <NA>
#> miniUI                                                                                                                                                                                                                                                            <NA>
#> minqa                                                                                                                                                                                                                                                             <NA>
#> mitools                                                                                                                                                                                                                                                           <NA>
#> mlbench                                                                                                                                                                                                                                                           <NA>
#> mlr                                                                                                                                                                                                                                                               <NA>
#> mnormt                                                                                                                                                                                                                                                            <NA>
#> ModelMetrics                                                                                                                                                                                                                                                      <NA>
#> modelr                                                                                                                                                                                                                                                            <NA>
#> modeltools                                                                                                                                                                                                                                                        <NA>
#> moments                                                                                                                                                                                                                                                           <NA>
#> mRMRe                                                                                                                                                                                                                                                             <NA>
#> multcomp                                                                                                                                                                                                                                                          <NA>
#> munsell                                                                                                                                                                                                                                                           <NA>
#> mvtnorm                                                                                                                                                                                                                                                           <NA>
#> My.stepwise                                                                                                                                                                                                                                                       <NA>
#> naniar                                                                                                                                                                                                                                                            <NA>
#> networkD3                                                                                                                                                                                                                                                 knitr, shiny
#> nloptr                                                                                                                                                                                                                                                            <NA>
#> nnls                                                                                                                                                                                                                                                              <NA>
#> nondetects                                                                                                                                                                                                                                                        <NA>
#> norm                                                                                                                                                                                                                                                              <NA>
#> np                                                                                                                                                                                                                                                                <NA>
#> numDeriv                                                                                                                                                                                                                                                          <NA>
#> OmicSelector                                                                                                                                                                                                                                                      <NA>
#> openssl                                                                                                                                                                                                                                                           <NA>
#> org.Hs.eg.db                                                                                                                                                                                                                                                      <NA>
#> PairedData                                                                                                                                                                                                                                                        <NA>
#> pamr                                                                                                                                                                                                                                                              <NA>
#> pander                                                                                                                                                                                                                                                            <NA>
#> parallelly                                                                                                                                                                                                                                                        <NA>
#> parallelMap                                                                                                                                                                                                                                                       <NA>
#> ParamHelpers                                                                                                                                                                                                                                                      <NA>
#> ParBayesianOptimization                                                                                                                                                                                                                                           <NA>
#> parsetools                                                                                                                                                                                                                                                        <NA>
#> party                                                                                                                                                                                                                                                             <NA>
#> partykit                                                                                                                                                                                                                                                          <NA>
#> patchwork                                                                                                                                                                                                                                                         <NA>
#> pathview                                                                                                                                                                                                                                                          <NA>
#> pbivnorm                                                                                                                                                                                                                                                          <NA>
#> pbkrtest                                                                                                                                                                                                                                                          <NA>
#> pillar                                                                                                                                                                                                                                                            <NA>
#> pkgbuild                                                                                                                                                                                                                                                          <NA>
#> pkgcond                                                                                                                                                                                                                                                           <NA>
#> pkgconfig                                                                                                                                                                                                                                                         <NA>
#> pkgdown                                                                                                                                                                                                                                                           <NA>
#> pkgload                                                                                                                                                                                                                                                           <NA>
#> plogr                                                                                                                                                                                                                                                             <NA>
#> plotly                                                                                                                                                                                                                                                            <NA>
#> plyr                                                                                                                                                                                                                                                              <NA>
#> png                                                                                                                                                                                                                                                               <NA>
#> polspline                                                                                                                                                                                                                                                         <NA>
#> polyclip                                                                                                                                                                                                                                                          <NA>
#> polynom                                                                                                                                                                                                                                                           <NA>
#> postlogic                                                                                                                                                                                                                                                         <NA>
#> praise                                                                                                                                                                                                                                                            <NA>
#> preprocessCore                                                                                                                                                                                                                                                    <NA>
#> prettyunits                                                                                                                                                                                                                                                       <NA>
#> pROC                                                                                                                                                                                                                                                              <NA>
#> processx                                                                                                                                                                                                                                                          <NA>
#> prodlim                                                                                                                                                                                                                                                           <NA>
#> profileR                                                                                                                                                                                                                                                          <NA>
#> progress                                                                                                                                                                                                                                                          <NA>
#> progressr                                                                                                                                                                                                                                                         <NA>
#> promises                                                                                                                                                                                                                                                          <NA>
#> proxy                                                                                                                                                                                                                                                             <NA>
#> pryr                                                                                                                                                                                                                                                              <NA>
#> ps                                                                                                                                                                                                                                                                <NA>
#> psych                                                                                                                                                                                                                                                             <NA>
#> purrr                                                                                                                                                                                                                                                             <NA>
#> purrrogress                                                                                                                                                                                                                                                      dplyr
#> quadprog                                                                                                                                                                                                                                                          <NA>
#> quantmod                                                                                                                                                                                                                                                          <NA>
#> quantreg                                                                                                                                                                                                                                                          <NA>
#> questionr                                                                                                                                                                                                                                                         <NA>
#> qvalue                                                                                                                                                                                                                                                            <NA>
#> R.cache                                                                                                                                                                                                                                                           <NA>
#> R.methodsS3                                                                                                                                                                                                                                                       <NA>
#> R.oo                                                                                                                                                                                                                                                              <NA>
#> R.utils                                                                                                                                                                                                                                                           <NA>
#> R6                                                                                                                                                                                                                                                                <NA>
#> ragg                                                                                                                                                                                                                                                              <NA>
#> randomForest                                                                                                                                                                                                                                                      <NA>
#> ranger                                                                                                                                                                                                                                                            <NA>
#> RANN                                                                                                                                                                                                                                                              <NA>
#> rappdirs                                                                                                                                                                                                                                                          <NA>
#> rapportools                                                                                                                                                                                                                                                       <NA>
#> RBGL                                                                                                                                                                                                                                                              <NA>
#> rcmdcheck                                                                                                                                                                                                                                                         <NA>
#> RColorBrewer                                                                                                                                                                                                                                                      <NA>
#> Rcpp                                                                                                                                                                                                                                                              <NA>
#> RcppArmadillo                                                                                                                                                                                                                                                     <NA>
#> RcppEigen                                                                                                                                                                                                                                                         <NA>
#> RcppProgress                                                                                                                                                                                                                                                      <NA>
#> RcppTOML                                                                                                                                                                                                                                                          <NA>
#> RCurl                                                                                                                                                                                                                                                             <NA>
#> readr                                                                                                                                                                                                                                                             <NA>
#> readxl                                                                                                                                                                                                                                                            <NA>
#> recipes                                                                                                                                                                                                                                                           <NA>
#> rematch                                                                                                                                                                                                                                                           <NA>
#> rematch2                                                                                                                                                                                                                                                          <NA>
#> remotes                                                                                                                                                                                                                                                           <NA>
#> reprex                                                                                                                                                                                                                                                            <NA>
#> resample                                                                                                                                                                                                                                                          <NA>
#> reshape                                                                                                                                                                                                                                                           <NA>
#> reshape2                                                                                                                                                                                                                                                          <NA>
#> reticulate                                                                                                                                                                                                                                                        <NA>
#> rgl                                                                                                                                                                                                                                                              waldo
#> Rgraphviz                                                                                                                                                                                                                                                         <NA>
#> rhandsontable                                                                                                                                                                                                                                                     <NA>
#> rJava                                                                                                                                                                                                                                                             <NA>
#> rjson                                                                                                                                                                                                                                                             <NA>
#> rlang                                                                                                                                                                                                                                                            winch
#> rmarkdown                                                                                                                                                                                                                                                         <NA>
#> rms                                                                                                                                                                                                                                                               <NA>
#> robustbase                                                                                                                                                                                                                robustX, rrcov, matrixStats, quantreg, Hmisc
#> ROCR                                                                                                                                                                                                                                                              <NA>
#> ROSE                                                                                                                                                                                                                                                              <NA>
#> roxygen2                                                                                                                                                                                                                                                          <NA>
#> rprojroot                                                                                                                                                                                                                                                         <NA>
#> RSNNS                                                                                                                                                                                                                                                             <NA>
#> rsq                                                                                                                                                                                                                                                               <NA>
#> RSQLite                                                                                                                                                                                                                                                           <NA>
#> rstatix                                                                                                                                                                                                                                                           <NA>
#> rstudioapi                                                                                                                                                                                                                                                        <NA>
#> RUnit                                                                                                                                                                                                                                                             <NA>
#> rversions                                                                                                                                                                                                                                                         <NA>
#> rvest                                                                                                                                                                                                                                                             <NA>
#> RWeka                                                                                                                                                                                                                                                             <NA>
#> RWekajars                                                                                                                                                                                                                                                         <NA>
#> S4Vectors                                                                                                                                                                                                                                                         <NA>
#> sandwich                                                                                                                                                                                                                                                          <NA>
#> sass                                                                                                                                                                                                                                                              <NA>
#> scales                                                                                                                                                                                                                                                            <NA>
#> scatterpie                                                                                                                                                                                                                                                        <NA>
#> selectr                                                                                                                                                                                                                                                           <NA>
#> sessioninfo                                                                                                                                                                                                                                                       <NA>
#> shadowtext                                                                                                                                                                                                                                                        <NA>
#> shape                                                                                                                                                                                                                                                             <NA>
#> shiny                                                                                                                                                                                                                                                             <NA>
#> shinyfullscreen                                                                                                                                                                                                                                                   <NA>
#> shinyjqui                                                                                                                                                                                                                                                         <NA>
#> shinyjs                                                                                                                                                                                                                                                           <NA>
#> snow                                                                                                                                                                                                                                                              Rmpi
#> sourcetools                                                                                                                                                                                                                                                       <NA>
#> sp                                                                                                                                                                                                                                                                <NA>
#> SparseM                                                                                                                                                                                                                                                           <NA>
#> spFSR                                                                                                                                                                                                                                                             <NA>
#> SQUAREM                                                                                                                                                                                                                                                           <NA>
#> stabs                                                                                                                                                                                                                                                             <NA>
#> stargazer               AER, betareg, brglm, censReg, dynlm, eha, erer, ergm, fGarch,\ngee, glmx, gmm, lfe, lme4, lmtest, MASS, mclogit, mgcv, mlogit,\nnlme, nnet, ordinal, plm, pscl, quantreg, rms, relevent,\nrobustbase, sampleSelection, spdep, survey, survival
#> stringdist                                                                                                                                                                                                                                                        <NA>
#> stringi                                                                                                                                                                                                                                                           <NA>
#> stringr                                                                                                                                                                                                                                                           <NA>
#> strucchange                                                                                                                                                                                                                                                       <NA>
#> styler                                                                                                                                                                                                                                                            <NA>
#> SummarizedExperiment                                                                                                                                                                                                                                              <NA>
#> summarytools                                                                                                                                                                                                                                                      <NA>
#> survey                                                                                                                                                                                                                                                            <NA>
#> survminer                                                                                                                                                                                                                                                         <NA>
#> survMisc                                                                                                                                                                                                                                                          <NA>
#> sva                                                                                                                                                                                                                                                               <NA>
#> svglite                                                                                                                                                                                                                                                           <NA>
#> sys                                                                                                                                                                                                                                                               <NA>
#> systemfonts                                                                                                                                                                                                                                                       <NA>
#> tableone                                                                                                                                                                                                                                                          <NA>
#> TCGAbiolinks                                                                                                                                                                                                                                                      <NA>
#> TCGAbiolinksGUI.data                                                                                                                                                                                                                                              <NA>
#> tensorflow                                                                                                                                                                                                                                                        <NA>
#> testextra                                                                                                                                                                                                                                                         <NA>
#> testthat                                                                                                                                                                                                                                                          <NA>
#> textshaping                                                                                                                                                                                                                                                       <NA>
#> tfautograph                                                                                                                                                                                                                                                       <NA>
#> tfruns                                                                                                                                                                                                                                                            <NA>
#> TH.data                                                                                                                                                                                                                                                           <NA>
#> tibble                                                                                                                                                                                                                                                            <NA>
#> tictoc                                                                                                                                                                                                                                                            <NA>
#> tidygraph                                                                                                                                                                                                                                                         <NA>
#> tidyr                                                                                                                                                                                                                                                             <NA>
#> tidyselect                                                                                                                                                                                                                                                        <NA>
#> tidytemplate                                                                                                                                                                                                                                                      <NA>
#> tidytree                                                                                                                                                                                                                                                          <NA>
#> tidyverse                                                                                                                                                                                                                                                         <NA>
#> timeDate                                                                                                                                                                                                                                                          <NA>
#> tinytex                                                                                                                                                                                                                                                           <NA>
#> tmvnsim                                                                                                                                                                                                                                                           <NA>
#> treeio                                                                                                                                                                                                                                                            <NA>
#> TTR                                                                                                                                                                                                                                                           quantmod
#> tweenr                                                                                                                                                                                                                                                            <NA>
#> tzdb                                                                                                                                                                                                                                                              <NA>
#> UpSetR                                                                                                                                                                                                                                                            <NA>
#> usethis                                                                                                                                                                                                                                                           <NA>
#> utf8                                                                                                                                                                                                                                                              <NA>
#> uuid                                                                                                                                                                                                                                                              <NA>
#> varSelRF                                                                                                                                                                                                                                                          <NA>
#> vcd                                                                                                                                                                                                                                                               <NA>
#> vctrs                                                                                                                                                                                                                                                             <NA>
#> VennDiagram                                                                                                                                                                                                                                                       <NA>
#> VIM                                                                                                                                                                                                                                                               <NA>
#> viridis                                                                                                                                                                                                                                                           <NA>
#> viridisLite                                                                                                                                                                                                                                                       <NA>
#> visdat                                                                                                                                                                                                                                                            <NA>
#> vroom                                                                                                                                                                                                                                                             <NA>
#> waiter                                                                                                                                                                                                                                                            <NA>
#> waldo                                                                                                                                                                                                                                                             <NA>
#> webshot                                                                                                                                                                                                                                                           <NA>
#> whisker                                                                                                                                                                                                                                                           <NA>
#> withr                                                                                                                                                                                                                                                             <NA>
#> xfun                                                                                                                                                                                                                                                              <NA>
#> xgboost                                                                                                                                                                                                                                                           <NA>
#> xlsx                                                                                                                                                                                                                                                              <NA>
#> xlsxjars                                                                                                                                                                                                                                                          <NA>
#> XML                                                                                                                                                                                                                                                               <NA>
#> xml2                                                                                                                                                                                                                                                              <NA>
#> xopen                                                                                                                                                                                                                                                             <NA>
#> xtable                                                                                                                                                                                                                                                            <NA>
#> xts                                                                                                                                                                                                                                                               <NA>
#> XVector                                                                                                                                                                                                                                                           <NA>
#> yaml                                                                                                                                                                                                                                                              <NA>
#> yulab.utils                                                                                                                                                                                                                                                       <NA>
#> zeallot                                                                                                                                                                                                                                                           <NA>
#> zip                                                                                                                                                                                                                                                               <NA>
#> zlibbioc                                                                                                                                                                                                                                                          <NA>
#> zoo                                                                                                                                                                                                                                                               <NA>
#> base                                                                                                                                                                                                                                                              <NA>
#> boot                                                                                                                                                                                                                                                              <NA>
#> class                                                                                                                                                                                                                                                             <NA>
#> cluster                                                                                                                                                                                                                                                           <NA>
#> codetools                                                                                                                                                                                                                                                         <NA>
#> compiler                                                                                                                                                                                                                                                          <NA>
#> datasets                                                                                                                                                                                                                                                          <NA>
#> foreign                                                                                                                                                                                                                                                           <NA>
#> graphics                                                                                                                                                                                                                                                          <NA>
#> grDevices                                                                                                                                                                                                                                                         <NA>
#> grid                                                                                                                                                                                                                                                              <NA>
#> KernSmooth                                                                                                                                                                                                                                                        <NA>
#> lattice                                                                                                                                                                                                                                                          chron
#> MASS                                                                                                                                                                                                                                                              <NA>
#> Matrix                                                                                                                                                                                             MatrixModels, graph, SparseM, sfsmisc, igraph, maptools, sp,\nspdep
#> methods                                                                                                                                                                                                                                                           <NA>
#> mgcv                                                                                                                                                                                                                                                              <NA>
#> nlme                                                                                                                                                                                                                                                              <NA>
#> nnet                                                                                                                                                                                                                                                              <NA>
#> parallel                                                                                                                                                                                                                                               snow, nws, Rmpi
#> rpart                                                                                                                                                                                                                                                             <NA>
#> spatial                                                                                                                                                                                                                                                           <NA>
#> splines                                                                                                                                                                                                                                                           <NA>
#> stats                                                                                                                                                                                                                                                             <NA>
#> stats4                                                                                                                                                                                                                                                            <NA>
#> survival                                                                                                                                                                                                                                                          <NA>
#> tcltk                                                                                                                                                                                                                                                             <NA>
#> tools                                                                                                                                                                                                                                                             <NA>
#> utils                                                                                                                                                                                                                                                             <NA>
#>                                                        License
#> abind                                              LGPL (>= 2)
#> affy                                             LGPL (>= 2.0)
#> affyio                                             LGPL (>= 2)
#> annotate                                          Artistic-2.0
#> AnnotationDbi                                     Artistic-2.0
#> ape                                              GPL-2 | GPL-3
#> aplot                                             Artistic-2.0
#> arm                                                  GPL (> 2)
#> arules                                                   GPL-3
#> askpass                                     MIT + file LICENSE
#> assertthat                                               GPL-3
#> autokeras                                   MIT + file LICENSE
#> backports                                        GPL-2 | GPL-3
#> base64enc                                        GPL-2 | GPL-3
#> BBmisc                             BSD_2_clause + file LICENSE
#> BH                                                     BSL-1.0
#> Biobase                                           Artistic-2.0
#> BiocCheck                                         Artistic-2.0
#> BiocFileCache                                     Artistic-2.0
#> BiocGenerics                                      Artistic-2.0
#> BiocManager                                       Artistic-2.0
#> Biocomb                                             GPL (>= 3)
#> BiocParallel                                     GPL-2 | GPL-3
#> BiocStyle                                         Artistic-2.0
#> BiocVersion                                       Artistic-2.0
#> biocViews                                         Artistic-2.0
#> biomaRt                                           Artistic-2.0
#> Biostrings                                        Artistic-2.0
#> bit                                              GPL-2 | GPL-3
#> bit64                                            GPL-2 | GPL-3
#> bitops                                              GPL (>= 2)
#> blob                                        MIT + file LICENSE
#> bookdown                                                 GPL-3
#> Boruta                                              GPL (>= 2)
#> bounceR                                     MIT + file LICENSE
#> brew                                                     GPL-2
#> brio                                        MIT + file LICENSE
#> broom                                       MIT + file LICENSE
#> broom.helpers                                            GPL-3
#> bslib                                       MIT + file LICENSE
#> C50                                                      GPL-3
#> cachem                                      MIT + file LICENSE
#> calibrate                                                GPL-2
#> callr                                       MIT + file LICENSE
#> car                                                 GPL (>= 2)
#> carData                                             GPL (>= 2)
#> caret                                               GPL (>= 2)
#> caTools                                                  GPL-3
#> cellranger                                  MIT + file LICENSE
#> checkmate                          BSD_3_clause + file LICENSE
#> circlize                                    MIT + file LICENSE
#> classInt                                            GPL (>= 2)
#> cli                                         MIT + file LICENSE
#> clipr                                                    GPL-3
#> clue                                                     GPL-2
#> clusterProfiler                                   Artistic-2.0
#> coda                                                GPL (>= 2)
#> coin                                                     GPL-2
#> colorspace                         BSD_3_clause + file LICENSE
#> combinat                                                 GPL-2
#> commonmark                         BSD_2_clause + file LICENSE
#> ComplexHeatmap                              MIT + file LICENSE
#> config                                                   GPL-3
#> corrplot                                    MIT + file LICENSE
#> cowplot                                                  GPL-2
#> cpp11                                       MIT + file LICENSE
#> crayon                                      MIT + file LICENSE
#> credentials                                 MIT + file LICENSE
#> crosstalk                                   MIT + file LICENSE
#> cubature                                                 GPL-3
#> Cubist                                                   GPL-3
#> curl                                        MIT + file LICENSE
#> cutpointr                                                GPL-3
#> data.table                              MPL-2.0 | file LICENSE
#> DBI                                              LGPL (>= 2.1)
#> dbplyr                                      MIT + file LICENSE
#> dbscan                                              GPL (>= 2)
#> deepnet                                                    GPL
#> DelayedArray                                      Artistic-2.0
#> DEoptimR                                            GPL (>= 2)
#> Deriv                                               GPL (>= 3)
#> desc                                        MIT + file LICENSE
#> DESeq2                                             LGPL (>= 3)
#> devtools                                    MIT + file LICENSE
#> DiceKriging                                      GPL-2 | GPL-3
#> diffobj                                          GPL-2 | GPL-3
#> digest                                              GPL (>= 2)
#> DMwR                                                GPL (>= 2)
#> DO.db                                             Artistic-2.0
#> doParallel                                               GPL-2
#> DOSE                                              Artistic-2.0
#> downlit                                     MIT + file LICENSE
#> downloader                                               GPL-2
#> dplyr                                       MIT + file LICENSE
#> DT                                        GPL-3 | file LICENSE
#> dtplyr                                      MIT + file LICENSE
#> e1071                                            GPL-2 | GPL-3
#> edgeR                                                GPL (>=2)
#> ellipsis                                    MIT + file LICENSE
#> enrichplot                                        Artistic-2.0
#> entropy                                             GPL (>= 3)
#> epiDisplay                                          GPL (>= 2)
#> evaluate                                    MIT + file LICENSE
#> exactRankTests                                      GPL (>= 2)
#> fansi                                            GPL-2 | GPL-3
#> farver                                      MIT + file LICENSE
#> fastmap                                     MIT + file LICENSE
#> fastmatch                                                GPL-2
#> feseR                                     GPL-2 | file LICENSE
#> fgsea                                       MIT + file LICENCE
#> filelock                                    MIT + file LICENSE
#> fontawesome                                 MIT + file LICENSE
#> forcats                                     MIT + file LICENSE
#> foreach                                Apache License (== 2.0)
#> formatR                                                    GPL
#> Formula                                          GPL-2 | GPL-3
#> fs                                          MIT + file LICENSE
#> FSelector                                                GPL-2
#> funModeling                                              GPL-2
#> furrr                                       MIT + file LICENSE
#> futile.logger                                           LGPL-3
#> futile.options                                          LGPL-3
#> future                                           LGPL (>= 2.1)
#> future.apply                                        GPL (>= 2)
#> gargle                                      MIT + file LICENSE
#> gdata                                                    GPL-2
#> GDCRNATools                                       Artistic-2.0
#> genefilter                                        Artistic-2.0
#> geneplotter                                       Artistic-2.0
#> generics                                    MIT + file LICENSE
#> GenomeInfoDb                                      Artistic-2.0
#> GenomeInfoDbData                                  Artistic-2.0
#> GenomicDataCommons                                Artistic-2.0
#> GenomicRanges                                     Artistic-2.0
#> gert                                        MIT + file LICENSE
#> GetoptLong                                  MIT + file LICENSE
#> ggbiplot                                                 GPL-2
#> ggforce                                     MIT + file LICENSE
#> ggfun                                             Artistic-2.0
#> ggplot2                                     MIT + file LICENSE
#> ggplotify                                         Artistic-2.0
#> ggpubr                                                   GPL-2
#> ggraph                                      MIT + file LICENSE
#> ggrepel                                   GPL-3 | file LICENSE
#> ggsci                                     GPL-3 | file LICENSE
#> ggsignif                                  GPL-3 | file LICENSE
#> ggtext                                                   GPL-2
#> ggtree                                            Artistic-2.0
#> gh                                          MIT + file LICENSE
#> gitcreds                                    MIT + file LICENSE
#> gld                                                 GPL (>= 2)
#> glmnet                                                   GPL-2
#> GlobalOptions                               MIT + file LICENSE
#> globals                                          LGPL (>= 2.1)
#> glue                                        MIT + file LICENSE
#> gmodels                                                  GPL-2
#> GO.db                                             Artistic-2.0
#> googledrive                                 MIT + file LICENSE
#> googlesheets4                               MIT + file LICENSE
#> GOSemSim                                          Artistic-2.0
#> gower                                                    GPL-3
#> gplots                                                   GPL-2
#> graph                                             Artistic-2.0
#> graphlayouts                                MIT + file LICENSE
#> gridExtra                                           GPL (>= 2)
#> gridGraphics                                        GPL (>= 2)
#> gridtext                                    MIT + file LICENSE
#> gt                                          MIT + file LICENSE
#> gtable                                                   GPL-2
#> gtools                                                   GPL-2
#> gtsummary                                   MIT + file LICENSE
#> hardhat                                     MIT + file LICENSE
#> hash                                                GPL (>= 2)
#> haven                                       MIT + file LICENSE
#> here                                        MIT + file LICENSE
#> highr                                                      GPL
#> Hmisc                                               GPL (>= 2)
#> hms                                         MIT + file LICENSE
#> htmlTable                                           GPL (>= 3)
#> htmltools                                           GPL (>= 2)
#> htmlwidgets                                 MIT + file LICENSE
#> HTqPCR                                            Artistic-2.0
#> httpuv                               GPL (>= 2) | file LICENSE
#> httr                                        MIT + file LICENSE
#> ids                                         MIT + file LICENSE
#> igraph                                              GPL (>= 2)
#> imputeMissings                                      GPL (>= 2)
#> ini                                                      GPL-3
#> inum                                                     GPL-2
#> ipred                                               GPL (>= 2)
#> IRanges                                           Artistic-2.0
#> isoband                                     MIT + file LICENSE
#> iterators                              Apache License (== 2.0)
#> jpeg                                             GPL-2 | GPL-3
#> jquerylib                                   MIT + file LICENSE
#> jsonlite                                    MIT + file LICENSE
#> kableExtra                                  MIT + file LICENSE
#> KEGGgraph                                           GPL (>= 2)
#> KEGGREST                                          Artistic-2.0
#> keras                                       MIT + file LICENSE
#> kernlab                                                  GPL-2
#> klaR                                             GPL-2 | GPL-3
#> km.ci                                               GPL (>= 2)
#> KMsurv                                              GPL (>= 3)
#> knitr                                                      GPL
#> labeling                        MIT + file LICENSE | Unlimited
#> labelled                                                 GPL-3
#> laeken                                              GPL (>= 2)
#> lambda.r                                                LGPL-3
#> later                                       MIT + file LICENSE
#> latticeExtra                                        GPL (>= 2)
#> lava                                                     GPL-3
#> lavaan                                              GPL (>= 2)
#> lazyeval                                                 GPL-3
#> lhs                                                      GPL-3
#> libcoin                                                  GPL-2
#> lifecycle                                   MIT + file LICENSE
#> limma                                                GPL (>=2)
#> listenv                                          LGPL (>= 2.1)
#> lme4                                                GPL (>= 2)
#> lmom                         Common Public License Version 1.0
#> lmtest                                           GPL-2 | GPL-3
#> lobstr                                                   GPL-3
#> locfit                                              GPL (>= 2)
#> lubridate                                           GPL (>= 2)
#> magick                                      MIT + file LICENSE
#> magrittr                                    MIT + file LICENSE
#> maptools                                            GPL (>= 2)
#> markdown                                                 GPL-2
#> MatchIt                                             GPL (>= 2)
#> MatrixGenerics                                    Artistic-2.0
#> MatrixModels                                        GPL (>= 2)
#> matrixStats                                       Artistic-2.0
#> maxstat                                             GPL (>= 2)
#> mboost                                                   GPL-2
#> memoise                                     MIT + file LICENSE
#> mice                                             GPL-2 | GPL-3
#> mime                                                       GPL
#> miniUI                                                   GPL-3
#> minqa                                                    GPL-2
#> mitools                                                  GPL-2
#> mlbench                                                  GPL-2
#> mlr                                BSD_2_clause + file LICENSE
#> mnormt                                           GPL-2 | GPL-3
#> ModelMetrics                                        GPL (>= 2)
#> modelr                                                   GPL-3
#> modeltools                                               GPL-2
#> moments                                             GPL (>= 2)
#> mRMRe                                             Artistic-2.0
#> multcomp                                                 GPL-2
#> munsell                                     MIT + file LICENSE
#> mvtnorm                                                  GPL-2
#> My.stepwise                                         GPL (>= 3)
#> naniar                                      MIT + file LICENSE
#> networkD3                                           GPL (>= 3)
#> nloptr                                             LGPL (>= 3)
#> nnls                                                GPL (>= 2)
#> nondetects                                               GPL-3
#> norm                                                GPL (>= 2)
#> np                                                         GPL
#> numDeriv                                                 GPL-2
#> OmicSelector                       License: MIT + file LICENSE
#> openssl                                     MIT + file LICENSE
#> org.Hs.eg.db                                      Artistic-2.0
#> PairedData                                          GPL (>= 2)
#> pamr                                                     GPL-2
#> pander                                   AGPL-3 | file LICENSE
#> parallelly                                       LGPL (>= 2.1)
#> parallelMap                        BSD_2_clause + file LICENSE
#> ParamHelpers                       BSD_2_clause + file LICENSE
#> ParBayesianOptimization                                  GPL-2
#> parsetools                                               GPL-2
#> party                                                    GPL-2
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#> pkgdown                                     MIT + file LICENSE
#> pkgload                                                  GPL-3
#> plogr                                       MIT + file LICENSE
#> plotly                                      MIT + file LICENSE
#> plyr                                        MIT + file LICENSE
#> png                                              GPL-2 | GPL-3
#> polspline                                           GPL (>= 2)
#> polyclip                                                   BSL
#> polynom                                                  GPL-2
#> postlogic                                                GPL-2
#> praise                                      MIT + file LICENSE
#> preprocessCore                                     LGPL (>= 2)
#> prettyunits                                 MIT + file LICENSE
#> pROC                                                GPL (>= 3)
#> processx                                    MIT + file LICENSE
#> prodlim                                             GPL (>= 2)
#> profileR                                            GPL (>= 2)
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#> ps                                          MIT + file LICENSE
#> psych                                               GPL (>= 2)
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#> purrrogress                                 MIT + file LICENSE
#> quadprog                                            GPL (>= 2)
#> quantmod                                                 GPL-3
#> quantreg                                            GPL (>= 2)
#> questionr                                           GPL (>= 2)
#> qvalue                                                    LGPL
#> R.cache                                          LGPL (>= 2.1)
#> R.methodsS3                                      LGPL (>= 2.1)
#> R.oo                                             LGPL (>= 2.1)
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#> R6                                          MIT + file LICENSE
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#> randomForest                                        GPL (>= 2)
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#> RANN                                                GPL (>= 3)
#> rappdirs                                    MIT + file LICENSE
#> rapportools                                             AGPL-3
#> RBGL                                              Artistic-2.0
#> rcmdcheck                                   MIT + file LICENSE
#> RColorBrewer                                Apache License 2.0
#> Rcpp                                                GPL (>= 2)
#> RcppArmadillo                                       GPL (>= 2)
#> RcppEigen                            GPL (>= 2) | file LICENSE
#> RcppProgress                                        GPL (>= 3)
#> RcppTOML                                            GPL (>= 2)
#> RCurl                              BSD_3_clause + file LICENSE
#> readr                                       MIT + file LICENSE
#> readxl                                      MIT + file LICENSE
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#> resample                           BSD_3_clause + file LICENSE
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#> reshape2                                    MIT + file LICENSE
#> reticulate                                  Apache License 2.0
#> rgl                                                        GPL
#> Rgraphviz                                                  EPL
#> rhandsontable                               MIT + file LICENSE
#> rJava                                                 LGPL-2.1
#> rjson                                                    GPL-2
#> rlang                                       MIT + file LICENSE
#> rmarkdown                                                GPL-3
#> rms                                                 GPL (>= 2)
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#> ROCR                                                GPL (>= 2)
#> ROSE                                                     GPL-2
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#> RSNNS                               LGPL (>= 2) | file LICENSE
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#> RSQLite                                          LGPL (>= 2.1)
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#> RWeka                                                    GPL-2
#> RWekajars                                                GPL-2
#> S4Vectors                                         Artistic-2.0
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#> sass                                        MIT + file LICENSE
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#> scatterpie                                        Artistic-2.0
#> selectr                            BSD_3_clause + file LICENCE
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#> shinyfullscreen                             MIT + file LICENSE
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#> shinyjs                                     MIT + file LICENSE
#> snow                                                       GPL
#> sourcetools                                 MIT + file LICENSE
#> sp                                                  GPL (>= 2)
#> SparseM                                             GPL (>= 2)
#> spFSR                                                    GPL-3
#> SQUAREM                                             GPL (>= 2)
#> stabs                                                    GPL-2
#> stargazer                                           GPL (>= 2)
#> stringdist                                               GPL-3
#> stringi                                           file LICENSE
#> stringr                                   GPL-2 | file LICENSE
#> strucchange                                      GPL-2 | GPL-3
#> styler                                      MIT + file LICENSE
#> SummarizedExperiment                              Artistic-2.0
#> summarytools                                             GPL-2
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#> survMisc                                                 GPL-2
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#> systemfonts                                 MIT + file LICENSE
#> tableone                                                 GPL-2
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#> TCGAbiolinksGUI.data                                     GPL-3
#> tensorflow                                  Apache License 2.0
#> testextra                                                GPL-2
#> testthat                                    MIT + file LICENSE
#> textshaping                                 MIT + file LICENSE
#> tfautograph                                              GPL-3
#> tfruns                                      Apache License 2.0
#> TH.data                                                  GPL-3
#> tibble                                      MIT + file LICENSE
#> tictoc                  Apache License (== 2.0) | file LICENSE
#> tidygraph                                   MIT + file LICENSE
#> tidyr                                       MIT + file LICENSE
#> tidyselect                                  MIT + file LICENSE
#> tidytemplate                                MIT + file LICENSE
#> tidytree                                          Artistic-2.0
#> tidyverse                                   MIT + file LICENSE
#> timeDate                                            GPL (>= 2)
#> tinytex                                     MIT + file LICENSE
#> tmvnsim                                                  GPL-2
#> treeio                                            Artistic-2.0
#> TTR                                                 GPL (>= 2)
#> tweenr                                      MIT + file LICENSE
#> tzdb                                        MIT + file LICENSE
#> UpSetR                                      MIT + file LICENSE
#> usethis                                     MIT + file LICENSE
#> utf8                    Apache License (== 2.0) | file LICENSE
#> uuid                                        MIT + file LICENSE
#> varSelRF                                            GPL (>= 2)
#> vcd                                                      GPL-2
#> vctrs                                       MIT + file LICENSE
#> VennDiagram                                              GPL-2
#> VIM                                                 GPL (>= 2)
#> viridis                                     MIT + file LICENSE
#> viridisLite                                 MIT + file LICENSE
#> visdat                                      MIT + file LICENSE
#> vroom                                       MIT + file LICENSE
#> waiter                                      MIT + file LICENSE
#> waldo                                       MIT + file LICENSE
#> webshot                                                  GPL-2
#> whisker                                                  GPL-3
#> withr                                       MIT + file LICENSE
#> xfun                                        MIT + file LICENSE
#> xgboost                 Apache License (== 2.0) | file LICENSE
#> xlsx                                                     GPL-3
#> xlsxjars                                                 GPL-3
#> XML                                BSD_3_clause + file LICENSE
#> xml2                                        MIT + file LICENSE
#> xopen                                       MIT + file LICENSE
#> xtable                                              GPL (>= 2)
#> xts                                                 GPL (>= 2)
#> XVector                                           Artistic-2.0
#> yaml                               BSD_3_clause + file LICENSE
#> yulab.utils                                       Artistic-2.0
#> zeallot                                     MIT + file LICENSE
#> zip                                         MIT + file LICENSE
#> zlibbioc                           Artistic-2.0 + file LICENSE
#> zoo                                              GPL-2 | GPL-3
#> base                                           Part of R 4.2.0
#> boot                                                 Unlimited
#> class                                            GPL-2 | GPL-3
#> cluster                                             GPL (>= 2)
#> codetools                                                  GPL
#> compiler                                       Part of R 4.2.0
#> datasets                                       Part of R 4.2.0
#> foreign                                             GPL (>= 2)
#> graphics                                       Part of R 4.2.0
#> grDevices                                      Part of R 4.2.0
#> grid                                           Part of R 4.2.0
#> KernSmooth                                           Unlimited
#> lattice                                             GPL (>= 2)
#> MASS                                             GPL-2 | GPL-3
#> Matrix                               GPL (>= 2) | file LICENCE
#> methods                                        Part of R 4.2.0
#> mgcv                                                GPL (>= 2)
#> nlme                                                GPL (>= 2)
#> nnet                                             GPL-2 | GPL-3
#> parallel                                       Part of R 4.2.0
#> rpart                                            GPL-2 | GPL-3
#> spatial                                          GPL-2 | GPL-3
#> splines                                        Part of R 4.2.0
#> stats                                          Part of R 4.2.0
#> stats4                                         Part of R 4.2.0
#> survival                                           LGPL (>= 2)
#> tcltk                                          Part of R 4.2.0
#> tools                                          Part of R 4.2.0
#> utils                                          Part of R 4.2.0
#>                         License_is_FOSS License_restricts_use OS_type
#> abind                              <NA>                  <NA>    <NA>
#> affy                               <NA>                  <NA>    <NA>
#> affyio                             <NA>                  <NA>    <NA>
#> annotate                           <NA>                  <NA>    <NA>
#> AnnotationDbi                      <NA>                  <NA>    <NA>
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#> aplot                              <NA>                  <NA>    <NA>
#> arm                                <NA>                  <NA>    <NA>
#> arules                             <NA>                  <NA>    <NA>
#> askpass                            <NA>                  <NA>    <NA>
#> assertthat                         <NA>                  <NA>    <NA>
#> autokeras                          <NA>                  <NA>    <NA>
#> backports                          <NA>                  <NA>    <NA>
#> base64enc                          <NA>                  <NA>    <NA>
#> BBmisc                             <NA>                  <NA>    <NA>
#> BH                                 <NA>                  <NA>    <NA>
#> Biobase                            <NA>                  <NA>    <NA>
#> BiocCheck                          <NA>                  <NA>    <NA>
#> BiocFileCache                      <NA>                  <NA>    <NA>
#> BiocGenerics                       <NA>                  <NA>    <NA>
#> BiocManager                        <NA>                  <NA>    <NA>
#> Biocomb                            <NA>                  <NA>    <NA>
#> BiocParallel                       <NA>                  <NA>    <NA>
#> BiocStyle                          <NA>                  <NA>    <NA>
#> BiocVersion                        <NA>                  <NA>    <NA>
#> biocViews                          <NA>                  <NA>    <NA>
#> biomaRt                            <NA>                  <NA>    <NA>
#> Biostrings                         <NA>                  <NA>    <NA>
#> bit                                <NA>                  <NA>    <NA>
#> bit64                              <NA>                  <NA>    <NA>
#> bitops                             <NA>                  <NA>    <NA>
#> blob                               <NA>                  <NA>    <NA>
#> bookdown                           <NA>                  <NA>    <NA>
#> Boruta                             <NA>                  <NA>    <NA>
#> bounceR                            <NA>                  <NA>    <NA>
#> brew                               <NA>                  <NA>    <NA>
#> brio                               <NA>                  <NA>    <NA>
#> broom                              <NA>                  <NA>    <NA>
#> broom.helpers                      <NA>                  <NA>    <NA>
#> bslib                              <NA>                  <NA>    <NA>
#> C50                                <NA>                  <NA>    <NA>
#> cachem                             <NA>                  <NA>    <NA>
#> calibrate                          <NA>                  <NA>    <NA>
#> callr                              <NA>                  <NA>    <NA>
#> car                                <NA>                  <NA>    <NA>
#> carData                            <NA>                  <NA>    <NA>
#> caret                              <NA>                  <NA>    <NA>
#> caTools                            <NA>                  <NA>    <NA>
#> cellranger                         <NA>                  <NA>    <NA>
#> checkmate                          <NA>                  <NA>    <NA>
#> circlize                           <NA>                  <NA>    <NA>
#> classInt                           <NA>                  <NA>    <NA>
#> cli                                <NA>                  <NA>    <NA>
#> clipr                              <NA>                  <NA>    <NA>
#> clue                               <NA>                  <NA>    <NA>
#> clusterProfiler                    <NA>                  <NA>    <NA>
#> coda                               <NA>                  <NA>    <NA>
#> coin                               <NA>                  <NA>    <NA>
#> colorspace                         <NA>                  <NA>    <NA>
#> combinat                           <NA>                  <NA>    <NA>
#> commonmark                         <NA>                  <NA>    <NA>
#> ComplexHeatmap                     <NA>                  <NA>    <NA>
#> config                             <NA>                  <NA>    <NA>
#> corrplot                           <NA>                  <NA>    <NA>
#> cowplot                            <NA>                  <NA>    <NA>
#> cpp11                              <NA>                  <NA>    <NA>
#> crayon                             <NA>                  <NA>    <NA>
#> credentials                        <NA>                  <NA>    <NA>
#> crosstalk                          <NA>                  <NA>    <NA>
#> cubature                           <NA>                  <NA>    <NA>
#> Cubist                             <NA>                  <NA>    <NA>
#> curl                               <NA>                  <NA>    <NA>
#> cutpointr                          <NA>                  <NA>    <NA>
#> data.table                         <NA>                  <NA>    <NA>
#> DBI                                <NA>                  <NA>    <NA>
#> dbplyr                             <NA>                  <NA>    <NA>
#> dbscan                             <NA>                  <NA>    <NA>
#> deepnet                            <NA>                  <NA>    <NA>
#> DelayedArray                       <NA>                  <NA>    <NA>
#> DEoptimR                           <NA>                  <NA>    <NA>
#> Deriv                              <NA>                  <NA>    <NA>
#> desc                               <NA>                  <NA>    <NA>
#> DESeq2                             <NA>                  <NA>    <NA>
#> devtools                           <NA>                  <NA>    <NA>
#> DiceKriging                        <NA>                  <NA>    <NA>
#> diffobj                            <NA>                  <NA>    <NA>
#> digest                             <NA>                  <NA>    <NA>
#> DMwR                               <NA>                  <NA>    <NA>
#> DO.db                              <NA>                  <NA>    <NA>
#> doParallel                         <NA>                  <NA>    <NA>
#> DOSE                               <NA>                  <NA>    <NA>
#> downlit                            <NA>                  <NA>    <NA>
#> downloader                         <NA>                  <NA>    <NA>
#> dplyr                              <NA>                  <NA>    <NA>
#> DT                                 <NA>                  <NA>    <NA>
#> dtplyr                             <NA>                  <NA>    <NA>
#> e1071                              <NA>                  <NA>    <NA>
#> edgeR                              <NA>                  <NA>    <NA>
#> ellipsis                           <NA>                  <NA>    <NA>
#> enrichplot                         <NA>                  <NA>    <NA>
#> entropy                            <NA>                  <NA>    <NA>
#> epiDisplay                         <NA>                  <NA>    <NA>
#> evaluate                           <NA>                  <NA>    <NA>
#> exactRankTests                     <NA>                  <NA>    <NA>
#> fansi                              <NA>                  <NA>    <NA>
#> farver                             <NA>                  <NA>    <NA>
#> fastmap                            <NA>                  <NA>    <NA>
#> fastmatch                          <NA>                  <NA>    <NA>
#> feseR                              <NA>                  <NA>    <NA>
#> fgsea                              <NA>                  <NA>    <NA>
#> filelock                           <NA>                  <NA>    <NA>
#> fontawesome                        <NA>                  <NA>    <NA>
#> forcats                            <NA>                  <NA>    <NA>
#> foreach                            <NA>                  <NA>    <NA>
#> formatR                            <NA>                  <NA>    <NA>
#> Formula                            <NA>                  <NA>    <NA>
#> fs                                 <NA>                  <NA>    <NA>
#> FSelector                          <NA>                  <NA>    <NA>
#> funModeling                        <NA>                  <NA>    <NA>
#> furrr                              <NA>                  <NA>    <NA>
#> futile.logger                      <NA>                  <NA>    <NA>
#> futile.options                     <NA>                  <NA>    <NA>
#> future                             <NA>                  <NA>    <NA>
#> future.apply                       <NA>                  <NA>    <NA>
#> gargle                             <NA>                  <NA>    <NA>
#> gdata                              <NA>                  <NA>    <NA>
#> GDCRNATools                        <NA>                  <NA>    <NA>
#> genefilter                         <NA>                  <NA>    <NA>
#> geneplotter                        <NA>                  <NA>    <NA>
#> generics                           <NA>                  <NA>    <NA>
#> GenomeInfoDb                       <NA>                  <NA>    <NA>
#> GenomeInfoDbData                   <NA>                  <NA>    <NA>
#> GenomicDataCommons                 <NA>                  <NA>    <NA>
#> GenomicRanges                      <NA>                  <NA>    <NA>
#> gert                               <NA>                  <NA>    <NA>
#> GetoptLong                         <NA>                  <NA>    <NA>
#> ggbiplot                           <NA>                  <NA>    <NA>
#> ggforce                            <NA>                  <NA>    <NA>
#> ggfun                              <NA>                  <NA>    <NA>
#> ggplot2                            <NA>                  <NA>    <NA>
#> ggplotify                          <NA>                  <NA>    <NA>
#> ggpubr                             <NA>                  <NA>    <NA>
#> ggraph                             <NA>                  <NA>    <NA>
#> ggrepel                            <NA>                  <NA>    <NA>
#> ggsci                              <NA>                  <NA>    <NA>
#> ggsignif                           <NA>                  <NA>    <NA>
#> ggtext                             <NA>                  <NA>    <NA>
#> ggtree                             <NA>                  <NA>    <NA>
#> gh                                 <NA>                  <NA>    <NA>
#> gitcreds                           <NA>                  <NA>    <NA>
#> gld                                <NA>                  <NA>    <NA>
#> glmnet                             <NA>                  <NA>    <NA>
#> GlobalOptions                      <NA>                  <NA>    <NA>
#> globals                            <NA>                  <NA>    <NA>
#> glue                               <NA>                  <NA>    <NA>
#> gmodels                            <NA>                  <NA>    <NA>
#> GO.db                              <NA>                  <NA>    <NA>
#> googledrive                        <NA>                  <NA>    <NA>
#> googlesheets4                      <NA>                  <NA>    <NA>
#> GOSemSim                           <NA>                  <NA>    <NA>
#> gower                              <NA>                  <NA>    <NA>
#> gplots                             <NA>                  <NA>    <NA>
#> graph                              <NA>                  <NA>    <NA>
#> graphlayouts                       <NA>                  <NA>    <NA>
#> gridExtra                          <NA>                  <NA>    <NA>
#> gridGraphics                       <NA>                  <NA>    <NA>
#> gridtext                           <NA>                  <NA>    <NA>
#> gt                                 <NA>                  <NA>    <NA>
#> gtable                             <NA>                  <NA>    <NA>
#> gtools                             <NA>                  <NA>    <NA>
#> gtsummary                          <NA>                  <NA>    <NA>
#> hardhat                            <NA>                  <NA>    <NA>
#> hash                               <NA>                  <NA>    <NA>
#> haven                              <NA>                  <NA>    <NA>
#> here                               <NA>                  <NA>    <NA>
#> highr                              <NA>                  <NA>    <NA>
#> Hmisc                              <NA>                  <NA>    <NA>
#> hms                                <NA>                  <NA>    <NA>
#> htmlTable                          <NA>                  <NA>    <NA>
#> htmltools                          <NA>                  <NA>    <NA>
#> htmlwidgets                        <NA>                  <NA>    <NA>
#> HTqPCR                             <NA>                  <NA>    <NA>
#> httpuv                             <NA>                  <NA>    <NA>
#> httr                               <NA>                  <NA>    <NA>
#> ids                                <NA>                  <NA>    <NA>
#> igraph                             <NA>                  <NA>    <NA>
#> imputeMissings                     <NA>                  <NA>    <NA>
#> ini                                <NA>                  <NA>    <NA>
#> inum                               <NA>                  <NA>    <NA>
#> ipred                              <NA>                  <NA>    <NA>
#> IRanges                            <NA>                  <NA>    <NA>
#> isoband                            <NA>                  <NA>    <NA>
#> iterators                          <NA>                  <NA>    <NA>
#> jpeg                               <NA>                  <NA>    <NA>
#> jquerylib                          <NA>                  <NA>    <NA>
#> jsonlite                           <NA>                  <NA>    <NA>
#> kableExtra                         <NA>                  <NA>    <NA>
#> KEGGgraph                          <NA>                  <NA>    <NA>
#> KEGGREST                           <NA>                  <NA>    <NA>
#> keras                              <NA>                  <NA>    <NA>
#> kernlab                            <NA>                  <NA>    <NA>
#> klaR                               <NA>                  <NA>    <NA>
#> km.ci                              <NA>                  <NA>    <NA>
#> KMsurv                             <NA>                  <NA>    <NA>
#> knitr                              <NA>                  <NA>    <NA>
#> labeling                           <NA>                  <NA>    <NA>
#> labelled                           <NA>                  <NA>    <NA>
#> laeken                             <NA>                  <NA>    <NA>
#> lambda.r                           <NA>                  <NA>    <NA>
#> later                              <NA>                  <NA>    <NA>
#> latticeExtra                       <NA>                  <NA>    <NA>
#> lava                               <NA>                  <NA>    <NA>
#> lavaan                             <NA>                  <NA>    <NA>
#> lazyeval                           <NA>                  <NA>    <NA>
#> lhs                                <NA>                  <NA>    <NA>
#> libcoin                            <NA>                  <NA>    <NA>
#> lifecycle                          <NA>                  <NA>    <NA>
#> limma                              <NA>                  <NA>    <NA>
#> listenv                            <NA>                  <NA>    <NA>
#> lme4                               <NA>                  <NA>    <NA>
#> lmom                               <NA>                  <NA>    <NA>
#> lmtest                             <NA>                  <NA>    <NA>
#> lobstr                             <NA>                  <NA>    <NA>
#> locfit                             <NA>                  <NA>    <NA>
#> lubridate                          <NA>                  <NA>    <NA>
#> magick                             <NA>                  <NA>    <NA>
#> magrittr                           <NA>                  <NA>    <NA>
#> maptools                           <NA>                  <NA>    <NA>
#> markdown                           <NA>                  <NA>    <NA>
#> MatchIt                            <NA>                  <NA>    <NA>
#> MatrixGenerics                     <NA>                  <NA>    <NA>
#> MatrixModels                       <NA>                  <NA>    <NA>
#> matrixStats                        <NA>                  <NA>    <NA>
#> maxstat                            <NA>                  <NA>    <NA>
#> mboost                             <NA>                  <NA>    <NA>
#> memoise                            <NA>                  <NA>    <NA>
#> mice                               <NA>                  <NA>    <NA>
#> mime                               <NA>                  <NA>    <NA>
#> miniUI                             <NA>                  <NA>    <NA>
#> minqa                              <NA>                  <NA>    <NA>
#> mitools                            <NA>                  <NA>    <NA>
#> mlbench                            <NA>                  <NA>    <NA>
#> mlr                                <NA>                  <NA>    <NA>
#> mnormt                             <NA>                  <NA>    <NA>
#> ModelMetrics                       <NA>                  <NA>    <NA>
#> modelr                             <NA>                  <NA>    <NA>
#> modeltools                         <NA>                  <NA>    <NA>
#> moments                            <NA>                  <NA>    <NA>
#> mRMRe                              <NA>                  <NA>    <NA>
#> multcomp                           <NA>                  <NA>    <NA>
#> munsell                            <NA>                  <NA>    <NA>
#> mvtnorm                            <NA>                  <NA>    <NA>
#> My.stepwise                        <NA>                  <NA>    <NA>
#> naniar                             <NA>                  <NA>    <NA>
#> networkD3                          <NA>                  <NA>    <NA>
#> nloptr                             <NA>                  <NA>    <NA>
#> nnls                               <NA>                  <NA>    <NA>
#> nondetects                         <NA>                  <NA>    <NA>
#> norm                               <NA>                  <NA>    <NA>
#> np                                 <NA>                  <NA>    <NA>
#> numDeriv                           <NA>                  <NA>    <NA>
#> OmicSelector                       <NA>                  <NA>    <NA>
#> openssl                            <NA>                  <NA>    <NA>
#> org.Hs.eg.db                       <NA>                  <NA>    <NA>
#> PairedData                         <NA>                  <NA>    <NA>
#> pamr                               <NA>                  <NA>    <NA>
#> pander                             <NA>                  <NA>    <NA>
#> parallelly                         <NA>                  <NA>    <NA>
#> parallelMap                        <NA>                  <NA>    <NA>
#> ParamHelpers                       <NA>                  <NA>    <NA>
#> ParBayesianOptimization            <NA>                  <NA>    <NA>
#> parsetools                         <NA>                  <NA>    <NA>
#> party                              <NA>                  <NA>    <NA>
#> partykit                           <NA>                  <NA>    <NA>
#> patchwork                          <NA>                  <NA>    <NA>
#> pathview                           <NA>                  <NA>    <NA>
#> pbivnorm                           <NA>                  <NA>    <NA>
#> pbkrtest                           <NA>                  <NA>    <NA>
#> pillar                             <NA>                  <NA>    <NA>
#> pkgbuild                           <NA>                  <NA>    <NA>
#> pkgcond                            <NA>                  <NA>    <NA>
#> pkgconfig                          <NA>                  <NA>    <NA>
#> pkgdown                            <NA>                  <NA>    <NA>
#> pkgload                            <NA>                  <NA>    <NA>
#> plogr                              <NA>                  <NA>    <NA>
#> plotly                             <NA>                  <NA>    <NA>
#> plyr                               <NA>                  <NA>    <NA>
#> png                                <NA>                  <NA>    <NA>
#> polspline                          <NA>                  <NA>    <NA>
#> polyclip                           <NA>                  <NA>    <NA>
#> polynom                            <NA>                  <NA>    <NA>
#> postlogic                          <NA>                  <NA>    <NA>
#> praise                             <NA>                  <NA>    <NA>
#> preprocessCore                     <NA>                  <NA>    <NA>
#> prettyunits                        <NA>                  <NA>    <NA>
#> pROC                               <NA>                  <NA>    <NA>
#> processx                           <NA>                  <NA>    <NA>
#> prodlim                            <NA>                  <NA>    <NA>
#> profileR                           <NA>                  <NA>    <NA>
#> progress                           <NA>                  <NA>    <NA>
#> progressr                          <NA>                  <NA>    <NA>
#> promises                           <NA>                  <NA>    <NA>
#> proxy                              <NA>                  <NA>    <NA>
#> pryr                               <NA>                  <NA>    <NA>
#> ps                                 <NA>                  <NA>    <NA>
#> psych                              <NA>                  <NA>    <NA>
#> purrr                              <NA>                  <NA>    <NA>
#> purrrogress                        <NA>                  <NA>    <NA>
#> quadprog                           <NA>                  <NA>    <NA>
#> quantmod                           <NA>                  <NA>    <NA>
#> quantreg                           <NA>                  <NA>    <NA>
#> questionr                          <NA>                  <NA>    <NA>
#> qvalue                             <NA>                  <NA>    <NA>
#> R.cache                            <NA>                  <NA>    <NA>
#> R.methodsS3                        <NA>                  <NA>    <NA>
#> R.oo                               <NA>                  <NA>    <NA>
#> R.utils                            <NA>                  <NA>    <NA>
#> R6                                 <NA>                  <NA>    <NA>
#> ragg                               <NA>                  <NA>    <NA>
#> randomForest                       <NA>                  <NA>    <NA>
#> ranger                             <NA>                  <NA>    <NA>
#> RANN                               <NA>                  <NA>    <NA>
#> rappdirs                           <NA>                  <NA>    <NA>
#> rapportools                        <NA>                  <NA>    <NA>
#> RBGL                               <NA>                  <NA>    <NA>
#> rcmdcheck                          <NA>                  <NA>    <NA>
#> RColorBrewer                       <NA>                  <NA>    <NA>
#> Rcpp                               <NA>                  <NA>    <NA>
#> RcppArmadillo                      <NA>                  <NA>    <NA>
#> RcppEigen                          <NA>                  <NA>    <NA>
#> RcppProgress                       <NA>                  <NA>    <NA>
#> RcppTOML                           <NA>                  <NA>    <NA>
#> RCurl                              <NA>                  <NA>    <NA>
#> readr                              <NA>                  <NA>    <NA>
#> readxl                             <NA>                  <NA>    <NA>
#> recipes                            <NA>                  <NA>    <NA>
#> rematch                            <NA>                  <NA>    <NA>
#> rematch2                           <NA>                  <NA>    <NA>
#> remotes                            <NA>                  <NA>    <NA>
#> reprex                             <NA>                  <NA>    <NA>
#> resample                           <NA>                  <NA>    <NA>
#> reshape                            <NA>                  <NA>    <NA>
#> reshape2                           <NA>                  <NA>    <NA>
#> reticulate                         <NA>                  <NA>    <NA>
#> rgl                                <NA>                  <NA>    <NA>
#> Rgraphviz                          <NA>                  <NA>    <NA>
#> rhandsontable                      <NA>                  <NA>    <NA>
#> rJava                              <NA>                  <NA>    <NA>
#> rjson                              <NA>                  <NA>    <NA>
#> rlang                              <NA>                  <NA>    <NA>
#> rmarkdown                          <NA>                  <NA>    <NA>
#> rms                                <NA>                  <NA>    <NA>
#> robustbase                         <NA>                  <NA>    <NA>
#> ROCR                               <NA>                  <NA>    <NA>
#> ROSE                               <NA>                  <NA>    <NA>
#> roxygen2                           <NA>                  <NA>    <NA>
#> rprojroot                          <NA>                  <NA>    <NA>
#> RSNNS                              <NA>                  <NA>    <NA>
#> rsq                                <NA>                  <NA>    <NA>
#> RSQLite                            <NA>                  <NA>    <NA>
#> rstatix                            <NA>                  <NA>    <NA>
#> rstudioapi                         <NA>                  <NA>    <NA>
#> RUnit                              <NA>                  <NA>    <NA>
#> rversions                          <NA>                  <NA>    <NA>
#> rvest                              <NA>                  <NA>    <NA>
#> RWeka                              <NA>                  <NA>    <NA>
#> RWekajars                          <NA>                  <NA>    <NA>
#> S4Vectors                          <NA>                  <NA>    <NA>
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#> scatterpie                         <NA>                  <NA>    <NA>
#> selectr                            <NA>                  <NA>    <NA>
#> sessioninfo                        <NA>                  <NA>    <NA>
#> shadowtext                         <NA>                  <NA>    <NA>
#> shape                              <NA>                  <NA>    <NA>
#> shiny                              <NA>                  <NA>    <NA>
#> shinyfullscreen                    <NA>                  <NA>    <NA>
#> shinyjqui                          <NA>                  <NA>    <NA>
#> shinyjs                            <NA>                  <NA>    <NA>
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#> SparseM                            <NA>                  <NA>    <NA>
#> spFSR                              <NA>                  <NA>    <NA>
#> SQUAREM                            <NA>                  <NA>    <NA>
#> stabs                              <NA>                  <NA>    <NA>
#> stargazer                          <NA>                  <NA>    <NA>
#> stringdist                         <NA>                  <NA>    <NA>
#> stringi                             yes                  <NA>    <NA>
#> stringr                            <NA>                  <NA>    <NA>
#> strucchange                        <NA>                  <NA>    <NA>
#> styler                             <NA>                  <NA>    <NA>
#> SummarizedExperiment               <NA>                  <NA>    <NA>
#> summarytools                       <NA>                  <NA>    <NA>
#> survey                             <NA>                  <NA>    <NA>
#> survminer                          <NA>                  <NA>    <NA>
#> survMisc                           <NA>                  <NA>    <NA>
#> sva                                <NA>                  <NA>    <NA>
#> svglite                            <NA>                  <NA>    <NA>
#> sys                                <NA>                  <NA>    <NA>
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#> TCGAbiolinks                       <NA>                  <NA>    <NA>
#> TCGAbiolinksGUI.data               <NA>                  <NA>    <NA>
#> tensorflow                         <NA>                  <NA>    <NA>
#> testextra                          <NA>                  <NA>    <NA>
#> testthat                           <NA>                  <NA>    <NA>
#> textshaping                        <NA>                  <NA>    <NA>
#> tfautograph                        <NA>                  <NA>    <NA>
#> tfruns                             <NA>                  <NA>    <NA>
#> TH.data                            <NA>                  <NA>    <NA>
#> tibble                             <NA>                  <NA>    <NA>
#> tictoc                             <NA>                  <NA>    <NA>
#> tidygraph                          <NA>                  <NA>    <NA>
#> tidyr                              <NA>                  <NA>    <NA>
#> tidyselect                         <NA>                  <NA>    <NA>
#> tidytemplate                       <NA>                  <NA>    <NA>
#> tidytree                           <NA>                  <NA>    <NA>
#> tidyverse                          <NA>                  <NA>    <NA>
#> timeDate                           <NA>                  <NA>    <NA>
#> tinytex                            <NA>                  <NA>    <NA>
#> tmvnsim                            <NA>                  <NA>    <NA>
#> treeio                             <NA>                  <NA>    <NA>
#> TTR                                <NA>                  <NA>    <NA>
#> tweenr                             <NA>                  <NA>    <NA>
#> tzdb                               <NA>                  <NA>    <NA>
#> UpSetR                             <NA>                  <NA>    <NA>
#> usethis                            <NA>                  <NA>    <NA>
#> utf8                               <NA>                  <NA>    <NA>
#> uuid                               <NA>                  <NA>    <NA>
#> varSelRF                           <NA>                  <NA>    <NA>
#> vcd                                <NA>                  <NA>    <NA>
#> vctrs                              <NA>                  <NA>    <NA>
#> VennDiagram                        <NA>                  <NA>    <NA>
#> VIM                                <NA>                  <NA>    <NA>
#> viridis                            <NA>                  <NA>    <NA>
#> viridisLite                        <NA>                  <NA>    <NA>
#> visdat                             <NA>                  <NA>    <NA>
#> vroom                              <NA>                  <NA>    <NA>
#> waiter                             <NA>                  <NA>    <NA>
#> waldo                              <NA>                  <NA>    <NA>
#> webshot                            <NA>                  <NA>    <NA>
#> whisker                            <NA>                  <NA>    <NA>
#> withr                              <NA>                  <NA>    <NA>
#> xfun                               <NA>                  <NA>    <NA>
#> xgboost                            <NA>                  <NA>    <NA>
#> xlsx                               <NA>                  <NA>    <NA>
#> xlsxjars                           <NA>                  <NA>    <NA>
#> XML                                <NA>                  <NA>    <NA>
#> xml2                               <NA>                  <NA>    <NA>
#> xopen                              <NA>                  <NA>    <NA>
#> xtable                             <NA>                  <NA>    <NA>
#> xts                                <NA>                  <NA>    <NA>
#> XVector                            <NA>                  <NA>    <NA>
#> yaml                               <NA>                  <NA>    <NA>
#> yulab.utils                        <NA>                  <NA>    <NA>
#> zeallot                            <NA>                  <NA>    <NA>
#> zip                                <NA>                  <NA>    <NA>
#> zlibbioc                           <NA>                  <NA>    <NA>
#> zoo                                <NA>                  <NA>    <NA>
#> base                               <NA>                  <NA>    <NA>
#> boot                               <NA>                  <NA>    <NA>
#> class                              <NA>                  <NA>    <NA>
#> cluster                            <NA>                  <NA>    <NA>
#> codetools                          <NA>                  <NA>    <NA>
#> compiler                           <NA>                  <NA>    <NA>
#> datasets                           <NA>                  <NA>    <NA>
#> foreign                            <NA>                  <NA>    <NA>
#> graphics                           <NA>                  <NA>    <NA>
#> grDevices                          <NA>                  <NA>    <NA>
#> grid                               <NA>                  <NA>    <NA>
#> KernSmooth                         <NA>                  <NA>    <NA>
#> lattice                            <NA>                  <NA>    <NA>
#> MASS                               <NA>                  <NA>    <NA>
#> Matrix                             <NA>                  <NA>    <NA>
#> methods                            <NA>                  <NA>    <NA>
#> mgcv                               <NA>                  <NA>    <NA>
#> nlme                               <NA>                  <NA>    <NA>
#> nnet                               <NA>                  <NA>    <NA>
#> parallel                           <NA>                  <NA>    <NA>
#> rpart                              <NA>                  <NA>    <NA>
#> spatial                            <NA>                  <NA>    <NA>
#> splines                            <NA>                  <NA>    <NA>
#> stats                              <NA>                  <NA>    <NA>
#> stats4                             <NA>                  <NA>    <NA>
#> survival                           <NA>                  <NA>    <NA>
#> tcltk                              <NA>                  <NA>    <NA>
#> tools                              <NA>                  <NA>    <NA>
#> utils                              <NA>                  <NA>    <NA>
#>                         MD5sum NeedsCompilation Built
#> abind                     <NA>               no 4.2.0
#> affy                      <NA>              yes 4.2.0
#> affyio                    <NA>              yes 4.2.0
#> annotate                  <NA>               no 4.2.0
#> AnnotationDbi             <NA>               no 4.2.0
#> ape                       <NA>              yes 4.2.0
#> aplot                     <NA>               no 4.2.0
#> arm                       <NA>               no 4.2.0
#> arules                    <NA>              yes 4.2.0
#> askpass                   <NA>              yes 4.2.0
#> assertthat                <NA>               no 4.2.0
#> autokeras                 <NA>               no 4.2.0
#> backports                 <NA>              yes 4.2.0
#> base64enc                 <NA>              yes 4.2.0
#> BBmisc                    <NA>              yes 4.2.0
#> BH                        <NA>               no 4.2.0
#> Biobase                   <NA>              yes 4.2.0
#> BiocCheck                 <NA>               no 4.2.0
#> BiocFileCache             <NA>               no 4.2.0
#> BiocGenerics              <NA>               no 4.2.0
#> BiocManager               <NA>               no 4.2.0
#> Biocomb                   <NA>              yes 4.2.0
#> BiocParallel              <NA>              yes 4.2.0
#> BiocStyle                 <NA>               no 4.2.0
#> BiocVersion               <NA>               no 4.2.0
#> biocViews                 <NA>               no 4.2.0
#> biomaRt                   <NA>               no 4.2.0
#> Biostrings                <NA>              yes 4.2.0
#> bit                       <NA>              yes 4.2.0
#> bit64                     <NA>              yes 4.2.0
#> bitops                    <NA>              yes 4.2.0
#> blob                      <NA>               no 4.2.0
#> bookdown                  <NA>               no 4.2.0
#> Boruta                    <NA>               no 4.2.0
#> bounceR                   <NA>               no 4.2.0
#> brew                      <NA>               no 4.2.0
#> brio                      <NA>              yes 4.2.0
#> broom                     <NA>               no 4.2.0
#> broom.helpers             <NA>               no 4.2.0
#> bslib                     <NA>               no 4.2.0
#> C50                       <NA>              yes 4.2.0
#> cachem                    <NA>              yes 4.2.0
#> calibrate                 <NA>               no 4.2.0
#> callr                     <NA>               no 4.2.0
#> car                       <NA>               no 4.2.0
#> carData                   <NA>               no 4.2.0
#> caret                     <NA>              yes 4.2.0
#> caTools                   <NA>              yes 4.2.0
#> cellranger                <NA>               no 4.2.0
#> checkmate                 <NA>              yes 4.2.0
#> circlize                  <NA>               no 4.2.0
#> classInt                  <NA>              yes 4.2.0
#> cli                       <NA>              yes 4.2.0
#> clipr                     <NA>               no 4.2.0
#> clue                      <NA>              yes 4.2.0
#> clusterProfiler           <NA>               no 4.2.0
#> coda                      <NA>               no 4.2.0
#> coin                      <NA>              yes 4.2.0
#> colorspace                <NA>              yes 4.2.0
#> combinat                  <NA>             <NA> 4.2.0
#> commonmark                <NA>              yes 4.2.0
#> ComplexHeatmap            <NA>               no 4.2.0
#> config                    <NA>               no 4.2.0
#> corrplot                  <NA>               no 4.2.0
#> cowplot                   <NA>               no 4.2.0
#> cpp11                     <NA>               no 4.2.0
#> crayon                    <NA>               no 4.2.0
#> credentials               <NA>               no 4.2.0
#> crosstalk                 <NA>               no 4.2.0
#> cubature                  <NA>              yes 4.2.0
#> Cubist                    <NA>              yes 4.2.0
#> curl                      <NA>              yes 4.2.0
#> cutpointr                 <NA>              yes 4.2.0
#> data.table                <NA>              yes 4.2.0
#> DBI                       <NA>               no 4.2.0
#> dbplyr                    <NA>               no 4.2.0
#> dbscan                    <NA>              yes 4.2.0
#> deepnet                   <NA>               no 4.2.0
#> DelayedArray              <NA>              yes 4.2.0
#> DEoptimR                  <NA>               no 4.2.0
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#> desc                      <NA>               no 4.2.0
#> DESeq2                    <NA>              yes 4.2.0
#> devtools                  <NA>               no 4.2.0
#> DiceKriging               <NA>              yes 4.2.0
#> diffobj                   <NA>              yes 4.2.0
#> digest                    <NA>              yes 4.2.0
#> DMwR                      <NA>               no 4.2.0
#> DO.db                     <NA>               no 4.2.0
#> doParallel                <NA>               no 4.2.0
#> DOSE                      <NA>               no 4.2.0
#> downlit                   <NA>               no 4.2.0
#> downloader                <NA>               no 4.2.0
#> dplyr                     <NA>              yes 4.2.0
#> DT                        <NA>               no 4.2.0
#> dtplyr                    <NA>               no 4.2.0
#> e1071                     <NA>              yes 4.2.0
#> edgeR                     <NA>              yes 4.2.0
#> ellipsis                  <NA>              yes 4.2.0
#> enrichplot                <NA>               no 4.2.0
#> entropy                   <NA>               no 4.2.0
#> epiDisplay                <NA>               no 4.2.0
#> evaluate                  <NA>               no 4.2.0
#> exactRankTests            <NA>              yes 4.2.0
#> fansi                     <NA>              yes 4.2.0
#> farver                    <NA>              yes 4.2.0
#> fastmap                   <NA>              yes 4.2.0
#> fastmatch                 <NA>              yes 4.2.0
#> feseR                     <NA>               no 4.2.0
#> fgsea                     <NA>              yes 4.2.0
#> filelock                  <NA>              yes 4.2.0
#> fontawesome               <NA>               no 4.2.0
#> forcats                   <NA>               no 4.2.0
#> foreach                   <NA>               no 4.2.0
#> formatR                   <NA>               no 4.2.0
#> Formula                   <NA>               no 4.2.0
#> fs                        <NA>              yes 4.2.0
#> FSelector                 <NA>               no 4.2.0
#> funModeling               <NA>               no 4.2.0
#> furrr                     <NA>               no 4.2.0
#> futile.logger             <NA>               no 4.2.0
#> futile.options            <NA>               no 4.2.0
#> future                    <NA>               no 4.2.0
#> future.apply              <NA>               no 4.2.0
#> gargle                    <NA>               no 4.2.0
#> gdata                     <NA>               no 4.2.0
#> GDCRNATools               <NA>               no 4.2.0
#> genefilter                <NA>              yes 4.2.0
#> geneplotter               <NA>               no 4.2.0
#> generics                  <NA>               no 4.2.0
#> GenomeInfoDb              <NA>               no 4.2.0
#> GenomeInfoDbData          <NA>               no 4.2.0
#> GenomicDataCommons        <NA>               no 4.2.0
#> GenomicRanges             <NA>              yes 4.2.0
#> gert                      <NA>              yes 4.2.0
#> GetoptLong                <NA>               no 4.2.0
#> ggbiplot                  <NA>               no 4.2.0
#> ggforce                   <NA>              yes 4.2.0
#> ggfun                     <NA>               no 4.2.0
#> ggplot2                   <NA>               no 4.2.0
#> ggplotify                 <NA>               no 4.2.0
#> ggpubr                    <NA>               no 4.2.0
#> ggraph                    <NA>              yes 4.2.0
#> ggrepel                   <NA>              yes 4.2.0
#> ggsci                     <NA>               no 4.2.0
#> ggsignif                  <NA>               no 4.2.0
#> ggtext                    <NA>               no 4.2.0
#> ggtree                    <NA>               no 4.2.0
#> gh                        <NA>               no 4.2.0
#> gitcreds                  <NA>               no 4.2.0
#> gld                       <NA>              yes 4.2.0
#> glmnet                    <NA>              yes 4.2.0
#> GlobalOptions             <NA>               no 4.2.0
#> globals                   <NA>               no 4.2.0
#> glue                      <NA>              yes 4.2.0
#> gmodels                   <NA>               no 4.2.0
#> GO.db                     <NA>               no 4.2.0
#> googledrive               <NA>               no 4.2.0
#> googlesheets4             <NA>               no 4.2.0
#> GOSemSim                  <NA>              yes 4.2.0
#> gower                     <NA>              yes 4.2.0
#> gplots                    <NA>               no 4.2.0
#> graph                     <NA>              yes 4.2.0
#> graphlayouts              <NA>              yes 4.2.0
#> gridExtra                 <NA>               no 4.2.0
#> gridGraphics              <NA>               no 4.2.0
#> gridtext                  <NA>              yes 4.2.0
#> gt                        <NA>               no 4.2.0
#> gtable                    <NA>               no 4.2.0
#> gtools                    <NA>              yes 4.2.0
#> gtsummary                 <NA>               no 4.2.0
#> hardhat                   <NA>               no 4.2.0
#> hash                      <NA>               no 4.2.0
#> haven                     <NA>              yes 4.2.0
#> here                      <NA>               no 4.2.0
#> highr                     <NA>               no 4.2.0
#> Hmisc                     <NA>              yes 4.2.0
#> hms                       <NA>               no 4.2.0
#> htmlTable                 <NA>               no 4.2.0
#> htmltools                 <NA>              yes 4.2.0
#> htmlwidgets               <NA>               no 4.2.0
#> HTqPCR                    <NA>               no 4.2.0
#> httpuv                    <NA>              yes 4.2.0
#> httr                      <NA>               no 4.2.0
#> ids                       <NA>               no 4.2.0
#> igraph                    <NA>              yes 4.2.0
#> imputeMissings            <NA>               no 4.2.0
#> ini                       <NA>               no 4.2.0
#> inum                      <NA>               no 4.2.0
#> ipred                     <NA>              yes 4.2.0
#> IRanges                   <NA>              yes 4.2.0
#> isoband                   <NA>              yes 4.2.0
#> iterators                 <NA>               no 4.2.0
#> jpeg                      <NA>              yes 4.2.0
#> jquerylib                 <NA>               no 4.2.0
#> jsonlite                  <NA>              yes 4.2.0
#> kableExtra                <NA>               no 4.2.0
#> KEGGgraph                 <NA>               no 4.2.0
#> KEGGREST                  <NA>               no 4.2.0
#> keras                     <NA>               no 4.2.0
#> kernlab                   <NA>              yes 4.2.0
#> klaR                      <NA>               no 4.2.0
#> km.ci                     <NA>               no 4.2.0
#> KMsurv                    <NA>             <NA> 4.2.0
#> knitr                     <NA>               no 4.2.0
#> labeling                  <NA>               no 4.2.0
#> labelled                  <NA>               no 4.2.0
#> laeken                    <NA>               no 4.2.0
#> lambda.r                  <NA>               no 4.2.0
#> later                     <NA>              yes 4.2.0
#> latticeExtra              <NA>               no 4.2.0
#> lava                      <NA>               no 4.2.0
#> lavaan                    <NA>               no 4.2.0
#> lazyeval                  <NA>              yes 4.2.0
#> lhs                       <NA>              yes 4.2.0
#> libcoin                   <NA>              yes 4.2.0
#> lifecycle                 <NA>               no 4.2.0
#> limma                     <NA>              yes 4.2.0
#> listenv                   <NA>               no 4.2.0
#> lme4                      <NA>              yes 4.2.0
#> lmom                      <NA>              yes 4.2.0
#> lmtest                    <NA>              yes 4.2.0
#> lobstr                    <NA>              yes 4.2.0
#> locfit                    <NA>              yes 4.2.0
#> lubridate                 <NA>              yes 4.2.0
#> magick                    <NA>              yes 4.2.0
#> magrittr                  <NA>              yes 4.2.0
#> maptools                  <NA>              yes 4.2.0
#> markdown                  <NA>              yes 4.2.0
#> MatchIt                   <NA>              yes 4.2.0
#> MatrixGenerics            <NA>               no 4.2.0
#> MatrixModels              <NA>               no 4.2.0
#> matrixStats               <NA>              yes 4.2.0
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#> mboost                    <NA>              yes 4.2.0
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#> mice                      <NA>              yes 4.2.0
#> mime                      <NA>              yes 4.2.0
#> miniUI                    <NA>               no 4.2.0
#> minqa                     <NA>              yes 4.2.0
#> mitools                   <NA>               no 4.2.0
#> mlbench                   <NA>              yes 4.2.0
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#> ModelMetrics              <NA>              yes 4.2.0
#> modelr                    <NA>               no 4.2.0
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#> munsell                   <NA>               no 4.2.0
#> mvtnorm                   <NA>              yes 4.2.0
#> My.stepwise               <NA>               no 4.2.0
#> naniar                    <NA>               no 4.2.0
#> networkD3                 <NA>               no 4.2.0
#> nloptr                    <NA>              yes 4.2.0
#> nnls                      <NA>             <NA> 4.2.0
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#> norm                      <NA>              yes 4.2.0
#> np                        <NA>              yes 4.2.0
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#> OmicSelector              <NA>               no 4.2.0
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#> party                     <NA>              yes 4.2.0
#> partykit                  <NA>              yes 4.2.0
#> patchwork                 <NA>               no 4.2.0
#> pathview                  <NA>               no 4.2.0
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#> pkgbuild                  <NA>               no 4.2.0
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#> pkgdown                   <NA>               no 4.2.0
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#> plotly                    <NA>               no 4.2.0
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#> png                       <NA>              yes 4.2.0
#> polspline                 <NA>              yes 4.2.0
#> polyclip                  <NA>              yes 4.2.0
#> polynom                   <NA>               no 4.2.0
#> postlogic                 <NA>               no 4.2.0
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#> preprocessCore            <NA>              yes 4.2.0
#> prettyunits               <NA>               no 4.2.0
#> pROC                      <NA>              yes 4.2.0
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#> proxy                     <NA>              yes 4.2.0
#> pryr                      <NA>              yes 4.2.0
#> ps                        <NA>              yes 4.2.0
#> psych                     <NA>               no 4.2.0
#> purrr                     <NA>              yes 4.2.0
#> purrrogress               <NA>               no 4.2.0
#> quadprog                  <NA>              yes 4.2.0
#> quantmod                  <NA>               no 4.2.0
#> quantreg                  <NA>              yes 4.2.0
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#> R.oo                      <NA>               no 4.2.0
#> R.utils                   <NA>               no 4.2.0
#> R6                        <NA>               no 4.2.0
#> ragg                      <NA>              yes 4.2.0
#> randomForest              <NA>              yes 4.2.0
#> ranger                    <NA>              yes 4.2.0
#> RANN                      <NA>              yes 4.2.0
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#> RBGL                      <NA>              yes 4.2.0
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#> RcppEigen                 <NA>              yes 4.2.0
#> RcppProgress              <NA>               no 4.2.0
#> RcppTOML                  <NA>              yes 4.2.0
#> RCurl                     <NA>              yes 4.2.0
#> readr                     <NA>              yes 4.2.0
#> readxl                    <NA>              yes 4.2.0
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#> rematch2                  <NA>               no 4.2.0
#> remotes                   <NA>               no 4.2.0
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#> resample                  <NA>               no 4.2.0
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#> reticulate                <NA>              yes 4.2.0
#> rgl                       <NA>              yes 4.2.0
#> Rgraphviz                 <NA>              yes 4.2.0
#> rhandsontable             <NA>               no 4.2.0
#> rJava                     <NA>              yes 4.2.0
#> rjson                     <NA>              yes 4.2.0
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#> rmarkdown                 <NA>               no 4.2.0
#> rms                       <NA>              yes 4.2.0
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#> ROCR                      <NA>               no 4.2.0
#> ROSE                      <NA>               no 4.2.0
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#> rprojroot                 <NA>               no 4.2.0
#> RSNNS                     <NA>              yes 4.2.0
#> rsq                       <NA>               no 4.2.0
#> RSQLite                   <NA>              yes 4.2.0
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#> RUnit                     <NA>               no 4.2.0
#> rversions                 <NA>               no 4.2.0
#> rvest                     <NA>               no 4.2.0
#> RWeka                     <NA>               no 4.2.0
#> RWekajars                 <NA>               no 4.2.0
#> S4Vectors                 <NA>              yes 4.2.0
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#> sass                      <NA>              yes 4.2.0
#> scales                    <NA>               no 4.2.0
#> scatterpie                <NA>               no 4.2.0
#> selectr                   <NA>               no 4.2.0
#> sessioninfo               <NA>               no 4.2.0
#> shadowtext                <NA>               no 4.2.0
#> shape                     <NA>               no 4.2.0
#> shiny                     <NA>               no 4.2.0
#> shinyfullscreen           <NA>               no 4.2.0
#> shinyjqui                 <NA>               no 4.2.0
#> shinyjs                   <NA>               no 4.2.0
#> snow                      <NA>               no 4.2.0
#> sourcetools               <NA>              yes 4.2.0
#> sp                        <NA>              yes 4.2.0
#> SparseM                   <NA>              yes 4.2.0
#> spFSR                     <NA>               no 4.2.0
#> SQUAREM                   <NA>               no 4.2.0
#> stabs                     <NA>               no 4.2.0
#> stargazer                 <NA>               no 4.2.0
#> stringdist                <NA>              yes 4.2.0
#> stringi                   <NA>              yes 4.2.0
#> stringr                   <NA>               no 4.2.0
#> strucchange               <NA>              yes 4.2.0
#> styler                    <NA>               no 4.2.0
#> SummarizedExperiment      <NA>               no 4.2.0
#> summarytools              <NA>               no 4.2.0
#> survey                    <NA>               no 4.2.0
#> survminer                 <NA>               no 4.2.0
#> survMisc                  <NA>               no 4.2.0
#> sva                       <NA>              yes 4.2.0
#> svglite                   <NA>              yes 4.2.0
#> sys                       <NA>              yes 4.2.0
#> systemfonts               <NA>              yes 4.2.0
#> tableone                  <NA>               no 4.2.0
#> TCGAbiolinks              <NA>               no 4.2.0
#> TCGAbiolinksGUI.data      <NA>               no 4.2.0
#> tensorflow                <NA>               no 4.2.0
#> testextra                 <NA>               no 4.2.0
#> testthat                  <NA>              yes 4.2.0
#> textshaping               <NA>              yes 4.2.0
#> tfautograph               <NA>               no 4.2.0
#> tfruns                    <NA>               no 4.2.0
#> TH.data                   <NA>               no 4.2.0
#> tibble                    <NA>              yes 4.2.0
#> tictoc                    <NA>               no 4.2.0
#> tidygraph                 <NA>              yes 4.2.0
#> tidyr                     <NA>              yes 4.2.0
#> tidyselect                <NA>              yes 4.2.0
#> tidytemplate              <NA>               no 4.2.0
#> tidytree                  <NA>               no 4.2.0
#> tidyverse                 <NA>               no 4.2.0
#> timeDate                  <NA>               no 4.2.0
#> tinytex                   <NA>               no 4.2.0
#> tmvnsim                   <NA>              yes 4.2.0
#> treeio                    <NA>               no 4.2.0
#> TTR                       <NA>              yes 4.2.0
#> tweenr                    <NA>              yes 4.2.0
#> tzdb                      <NA>              yes 4.2.0
#> UpSetR                    <NA>               no 4.2.0
#> usethis                   <NA>               no 4.2.0
#> utf8                      <NA>              yes 4.2.0
#> uuid                      <NA>              yes 4.2.0
#> varSelRF                  <NA>               no 4.2.0
#> vcd                       <NA>               no 4.2.0
#> vctrs                     <NA>              yes 4.2.0
#> VennDiagram               <NA>               no 4.2.0
#> VIM                       <NA>              yes 4.2.0
#> viridis                   <NA>               no 4.2.0
#> viridisLite               <NA>               no 4.2.0
#> visdat                    <NA>               no 4.2.0
#> vroom                     <NA>              yes 4.2.0
#> waiter                    <NA>               no 4.2.0
#> waldo                     <NA>               no 4.2.0
#> webshot                   <NA>               no 4.2.0
#> whisker                   <NA>               no 4.2.0
#> withr                     <NA>               no 4.2.0
#> xfun                      <NA>              yes 4.2.0
#> xgboost                   <NA>              yes 4.2.0
#> xlsx                      <NA>               no 4.2.0
#> xlsxjars                  <NA>               no 4.2.0
#> XML                       <NA>              yes 4.2.0
#> xml2                      <NA>              yes 4.2.0
#> xopen                     <NA>               no 4.2.0
#> xtable                    <NA>               no 4.2.0
#> xts                       <NA>              yes 4.2.0
#> XVector                   <NA>              yes 4.2.0
#> yaml                      <NA>              yes 4.2.0
#> yulab.utils               <NA>               no 4.2.0
#> zeallot                   <NA>               no 4.2.0
#> zip                       <NA>              yes 4.2.0
#> zlibbioc                  <NA>              yes 4.2.0
#> zoo                       <NA>              yes 4.2.0
#> base                      <NA>             <NA> 4.2.0
#> boot                      <NA>               no 4.0.5
#> class                     <NA>              yes 4.1.2
#> cluster                   <NA>              yes 4.1.3
#> codetools                 <NA>               no 4.0.3
#> compiler                  <NA>             <NA> 4.2.0
#> datasets                  <NA>             <NA> 4.2.0
#> foreign                   <NA>              yes 4.1.2
#> graphics                  <NA>              yes 4.2.0
#> grDevices                 <NA>              yes 4.2.0
#> grid                      <NA>              yes 4.2.0
#> KernSmooth                <NA>              yes 4.0.5
#> lattice                   <NA>              yes 4.2.0
#> MASS                      <NA>              yes 4.2.0
#> Matrix                    <NA>              yes 4.1.3
#> methods                   <NA>              yes 4.2.0
#> mgcv                      <NA>              yes 4.1.3
#> nlme                      <NA>              yes 4.1.3
#> nnet                      <NA>              yes 4.1.2
#> parallel                  <NA>              yes 4.2.0
#> rpart                     <NA>              yes 4.1.2
#> spatial                   <NA>              yes 4.0.0
#> splines                   <NA>              yes 4.2.0
#> stats                     <NA>              yes 4.2.0
#> stats4                    <NA>             <NA> 4.2.0
#> survival                  <NA>              yes 4.1.1
#> tcltk                     <NA>              yes 4.2.0
#> tools                     <NA>              yes 4.2.0
#> utils                     <NA>              yes 4.2.0

Clean the temporary and model files (as the tutorial results are simplified, and we do not need them).

unlink("temp", recursive = TRUE)
unlink("models", recursive = TRUE)
unlink("task.log")
unlink("mixed*.csv")