OmicSelector: Deep learning tutorial.
Konrad Stawiski
Department of Biostatistics and Translational Research, Medical University of Lodz, Lodz, Poland (https://biostat.umed.pl)konrad@konsta.com.pl Source:
vignettes/DeepLearningTutorial.Rmd
DeepLearningTutorial.RmdOutline
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:
OmicSelector_deep_learning = function(selected_miRNAs = ".",
wd = getwd(),
SMOTE = F,
keras_batch_size = 64,
clean_temp_files = T,
save_threshold_trainacc = 0.85,
save_threshold_testacc = 0.8,
keras_epochae = 5000,
keras_epoch = 2000,
keras_patience = 50,
hyperparameters = expand.grid(
layer1 = seq(3, 11, by = 2),
layer2 = c(0, seq(3, 11, by = 2)),
layer3 c(0, seq(3, 11, by = 2)),
activation_function_layer1 = c("relu", "sigmoid"),
activation_function_layer2 = c("relu", "sigmoid"),
activation_function_layer3 = c("relu", "sigmoid"),
dropout_layer1 = c(0, 0.1),
dropout_layer2 = c(0, 0.1),
dropout_layer3 = c(0),
layer1_regularizer = c(T, F),
layer2_regularizer = c(T, F),
layer3_regularizer = c(T, F),
optimizer = c("adam", "rmsprop", "sgd"),
autoencoder = c(0, 7, -7),
balanced = SMOTE,
formula = as.character(OmicSelector_create_formula(selected_miRNAs))[3],
scaled = c(T, F),
stringsAsFactors = F
),
add_features_to_predictions = F,
keras_threads = ceiling(parallel::detectCores() /
2),
start = 1,
end = nrow(hyperparameters),
output_file = "deeplearning_results.csv",
save_all_vars = F)
OmicSelector_load_datamix()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 binaryClassvariables (with valuesCaseandControl) and features of interest (starting with prefixhsa). -
SMOTE- logical parameter defining if the balanced training set should be used in the analysis. If set toFALSE, the function will usemixed_train.csvas a training set without any modification. If set toTRUEa balanced dataset will be used. Balancing is based onOmicSelector_load_datamix()function. -
clean_temp_files- logical parameter defining if the temporary files (from directorytemp-deeplearning) should be deleted after the function finishes. As best neural networks are saved in separatemodelsdirectory, we advise keeping thisTRUE. Setting it toFALSEmay 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 toFALSE. -
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 value2is 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 to0= none. -
layer3- number of neurons in third hidden layer. If set to0= 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 recommendadam. -
autoencoder- if and with how many neurons the autoencoder should be used in structure network. If set to0- 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 theautoencoderparameter (4in this example). If set to <0, e.g.-4the 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 usingas.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 ofhyperparametersdata frame should we start? -
end- at which row ofhyperparametersdata 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)Training with grid search
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 aCase. - 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 (
Caseas 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
.zipsuffix this will represent the model filename inmodels/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:
OmicSelector_deep_learning_predict = function(model_path = "our_models/model5.zip",
new_dataset = data.table::fread("Data/ks_data.csv"),
new_scaling = F,
old_train_csv_to_restore_scaling = NULL,
override_cutoff = NULL,
blinded = F)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 theClassvariable, you can set it toTRUE, 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 (pROCobject; can be used for plotting) -
roc_auc- AUC ROC -
model- model object (kerasobject) -
autoencoder- autoencoder model object (kerasobject)
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)
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#> Running under: Ubuntu 20.04.4 LTS
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#>
#> attached base packages:
#> [1] grid stats graphics grDevices utils datasets methods
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#>
#> 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
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#> [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
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#> [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
#> [112] cellranger_1.1.0 htmlTable_2.4.0 Deriv_4.1.3
#> [115] curl_4.3.2 nloptr_2.0.3 lifecycle_1.0.1
#> [118] nlme_3.1-157 jsonlite_1.8.0 desc_1.4.1
#> [121] fansi_1.0.3 pillar_1.7.0 fastmap_1.1.0
#> [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.rdsTo 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
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#> 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>
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#> tcltk <NA> yes 4.2.0
#> tools <NA> yes 4.2.0
#> utils <NA> yes 4.2.0Clean the temporary and model files (as the tutorial results are simplified, and we do not need them).