Installed R packages#
The following 958 packages are installed with R 4.4.0.
Last updated: November 13, 2024
| Package | Version | Description |
|---|---|---|
| abind | 1.4-5 | Combine Multidimensional Arrays |
| ade4 | 1.7-22 | Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences |
| admisc | 0.35 | Adrian Dusa's Miscellaneous |
| afex | 1.3-1 | Analysis of Factorial Experiments |
| affxparser | 1.74.0 | Affymetrix File Parsing SDK |
| affy | 1.80.0 | Methods for Affymetrix Oligonucleotide Arrays |
| affyio | 1.72.0 | Tools for parsing Affymetrix data files |
| airr | 1.5.0 | AIRR Data Representation Reference Library |
| alakazam | 1.3.0 | Immunoglobulin Clonal Lineage and Diversity Analysis |
| amap | 0.8-19 | Another Multidimensional Analysis Package |
| annotate | 1.80.0 | Annotation for microarrays |
| AnnotationDbi | 1.66.0 | Manipulation of SQLite-based annotations in Bioconductor |
| anytime | 0.3.9 | Anything to 'POSIXct' or 'Date' Converter |
| aod | 1.3.3 | Analysis of Overdispersed Data |
| ape | 5.8 | Analyses of Phylogenetics and Evolution |
| apeglm | 1.24.0 | Approximate posterior estimation for GLM coefficients |
| aplot | 0.2.2 | Decorate a 'ggplot' with Associated Information |
| argparser | 0.7.2 | Command-Line Argument Parser |
| arm | 1.14-4 | Data Analysis Using Regression and Multilevel/Hierarchical Models |
| arrayhelpers | 1.1-0 | Convenience Functions for Arrays |
| arrow | 15.0.1 | Integration to 'Apache' 'Arrow' |
| ashr | 2.2-63 | Methods for Adaptive Shrinkage, using Empirical Bayes |
| askpass | 1.2.0 | Password Entry Utilities for R, Git, and SSH |
| assertthat | 0.2.1 | Easy Pre and Post Assertions |
| babelgene | 22.9 | Gene Orthologs for Model Organisms in a Tidy Data Format |
| backbone | 2.1.3 | Extracts the Backbone from Graphs |
| backports | 1.4.1 | Reimplementations of Functions Introduced Since R-3.0.0 |
| base | 4.4.0 | The R Base Package |
| base64enc | 0.1-3 | Tools for base64 encoding |
| base64url | 1.4 | Fast and URL-Safe Base64 Encoder and Decoder |
| basefun | 1.1-4 | Infrastructure for Computing with Basis Functions |
| basilisk | 1.14.3 | Freezing Python Dependencies Inside Bioconductor Packages |
| basilisk.utils | 1.14.1 | Basilisk Installation Utilities |
| batchelor | 1.18.1 | Single-Cell Batch Correction Methods |
| bayesplot | 1.11.1 | Plotting for Bayesian Models |
| bayestestR | 0.13.2 | Understand and Describe Bayesian Models and Posterior Distributions |
| BBmisc | 1.13 | Miscellaneous Helper Functions for B. Bischl |
| bbmle | 1.0.25.1 | Tools for General Maximum Likelihood Estimation |
| bdsmatrix | 1.3-7 | Routines for Block Diagonal Symmetric Matrices |
| beachmat | 2.18.1 | Compiling Bioconductor to Handle Each Matrix Type |
| beeswarm | 0.4.0 | The Bee Swarm Plot, an Alternative to Stripchart |
| BgeeDB | 2.28.0 | Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology |
| BH | 1.84.0-0 | Boost C++ Header Files |
| bigD | 0.2.0 | Flexibly Format Dates and Times to a Given Locale |
| biglm | 0.9-2.1 | Bounded Memory Linear and Generalized Linear Models |
| bigmemory | 4.6.4 | Manage Massive Matrices with Shared Memory and Memory-Mapped Files |
| bigmemory.sri | 0.1.8 | A Shared Resource Interface for Bigmemory Project Packages |
| bio3d | 2.4-4 | Biological Structure Analysis |
| Biobase | 2.64.0 | Biobase: Base functions for Bioconductor |
| BiocFileCache | 2.10.2 | Manage Files Across Sessions |
| BiocGenerics | 0.50.0 | S4 generic functions used in Bioconductor |
| BiocIO | 1.12.0 | Standard Input and Output for Bioconductor Packages |
| BiocManager | 1.30.23 | Access the Bioconductor Project Package Repository |
| BiocNeighbors | 1.20.2 | Nearest Neighbor Detection for Bioconductor Packages |
| BiocParallel | 1.38.0 | Bioconductor facilities for parallel evaluation |
| BiocSingular | 1.18.0 | Singular Value Decomposition for Bioconductor Packages |
| BiocVersion | 3.19.1 | Set the appropriate version of Bioconductor packages |
| biocViews | 1.70.0 | Categorized views of R package repositories |
| biomaRt | 2.58.2 | Interface to BioMart databases (i.e. Ensembl) |
| Biostrings | 2.72.0 | Efficient manipulation of biological strings |
| biovizBase | 1.50.0 | Basic graphic utilities for visualization of genomic data. |
| bit | 4.0.5 | Classes and Methods for Fast Memory-Efficient Boolean Selections |
| bit64 | 4.0.5 | A S3 Class for Vectors of 64bit Integers |
| bitops | 1.0-7 | Bitwise Operations |
| blme | 1.0-5 | Bayesian Linear Mixed-Effects Models |
| blob | 1.2.4 | A Simple S3 Class for Representing Vectors of Binary Data ('BLOBS') |
| bmp | 0.3 | Read Windows Bitmap (BMP) Images |
| boot | 1.3-30 | Bootstrap Functions (Originally by Angelo Canty for S) |
| bootnet | 1.6 | Bootstrap Methods for Various Network Estimation Routines |
| brew | 1.0-10 | Templating Framework for Report Generation |
| bridgesampling | 1.1-2 | Bridge Sampling for Marginal Likelihoods and Bayes Factors |
| brio | 1.1.5 | Basic R Input Output |
| brms | 2.21.0 | Bayesian Regression Models using 'Stan' |
| Brobdingnag | 1.2-9 | Very Large Numbers in R |
| broom | 1.0.5 | Convert Statistical Objects into Tidy Tibbles |
| broom.helpers | 1.15.0 | Helpers for Model Coefficients Tibbles |
| bs4Dash | 2.3.3 | A 'Bootstrap 4' Version of 'shinydashboard' |
| BSgenome | 1.70.2 | Software infrastructure for efficient representation of full genomes and their SNPs |
| bslib | 0.7.0 | Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown' |
| ca | 0.71.1 | Simple, Multiple and Joint Correspondence Analysis |
| cachem | 1.0.8 | Cache R Objects with Automatic Pruning |
| Cairo | 1.6-2 | R Graphics Device using Cairo Graphics Library for Creating High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG, PostScript) and Display (X11 and Win32) Output |
| calibrate | 1.7.7 | Calibration of Scatterplot and Biplot Axes |
| callr | 3.7.6 | Call R from R |
| candisc | 0.9.0 | Visualizing Generalized Canonical Discriminant and Canonical Correlation Analysis |
| car | 3.1-2 | Companion to Applied Regression |
| carData | 3.0-5 | Companion to Applied Regression Data Sets |
| caret | 6.0-94 | Classification and Regression Training |
| caTools | 1.18.2 | Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc |
| CellChat | 2.1.2 | Inference and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics data |
| celldex | 1.12.0 | Reference Index for Cell Types |
| cellranger | 1.1.0 | Translate Spreadsheet Cell Ranges to Rows and Columns |
| checkmate | 2.3.1 | Fast and Versatile Argument Checks |
| ChIPseeker | 1.38.0 | ChIPseeker for ChIP peak Annotation, Comparison, and Visualization |
| chipseq | 1.52.0 | chipseq: A package for analyzing chipseq data |
| chk | 0.9.1 | Check User-Supplied Function Arguments |
| chromVAR | 1.24.0 | Chromatin Variation Across Regions |
| chron | 2.3-61 | Chronological Objects which Can Handle Dates and Times |
| circlize | 0.4.16 | Circular Visualization |
| class | 7.3-22 | Functions for Classification |
| classInt | 0.4-10 | Choose Univariate Class Intervals |
| cli | 3.6.2 | Helpers for Developing Command Line Interfaces |
| clipr | 0.8.0 | Read and Write from the System Clipboard |
| clock | 0.7.0 | Date-Time Types and Tools |
| clue | 0.3-65 | Cluster Ensembles |
| cluster | 2.1.6 | "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et al. |
| clusterProfiler | 4.10.1 | A universal enrichment tool for interpreting omics data |
| clustree | 0.5.1 | Visualise Clusterings at Different Resolutions |
| cmprsk | 2.2-11 | Subdistribution Analysis of Competing Risks |
| CNEr | 1.38.0 | CNE Detection and Visualization |
| cocor | 1.1-4 | Comparing Correlations |
| coda | 0.19-4.1 | Output Analysis and Diagnostics for MCMC |
| codetools | 0.2-20 | Code Analysis Tools for R |
| colorspace | 2.1-0 | A Toolbox for Manipulating and Assessing Colors and Palettes |
| colourpicker | 1.3.0 | A Colour Picker Tool for Shiny and for Selecting Colours in Plots |
| combinat | 0.0-8 | combinatorics utilities |
| commonmark | 1.9.1 | High Performance CommonMark and Github Markdown Rendering in R |
| comorbidity | 1.0.7 | Computing Comorbidity Scores |
| compiler | 4.4.0 | The R Compiler Package |
| ComplexHeatmap | 2.15.4 | Make Complex Heatmaps |
| conflicted | 1.2.0 | An Alternative Conflict Resolution Strategy |
| conquer | 1.3.3 | Convolution-Type Smoothed Quantile Regression |
| coro | 1.0.4 | 'Coroutines' for R |
| corpcor | 1.6.10 | Efficient Estimation of Covariance and (Partial) Correlation |
| corrplot | 0.92 | Visualization of a Correlation Matrix |
| covr | 3.6.4 | Test Coverage for Packages |
| cowplot | 1.1.3 | Streamlined Plot Theme and Plot Annotations for 'ggplot2' |
| coxme | 2.2-20 | Mixed Effects Cox Models |
| cpp11 | 0.4.7 | A C++11 Interface for R's C Interface |
| crayon | 1.5.2 | Colored Terminal Output |
| credentials | 2.0.1 | Tools for Managing SSH and Git Credentials |
| crossmatch | 1.3-1 | The Cross-match Test |
| crosstalk | 1.2.1 | Inter-Widget Interactivity for HTML Widgets |
| crul | 1.4.2 | HTTP Client |
| csaw | 1.36.1 | ChIP-Seq Analysis with Windows |
| cubature | 2.1.0 | Adaptive Multivariate Integration over Hypercubes |
| curl | 5.2.1 | A Modern and Flexible Web Client for R |
| data.table | 1.15.4 | Extension of data.frame |
| data.tree | 1.1.0 | General Purpose Hierarchical Data Structure |
| datasets | 4.4.0 | The R Datasets Package |
| datawizard | 0.10.0 | Easy Data Wrangling and Statistical Transformations |
| DBI | 1.2.2 | R Database Interface |
| dbparser | 2.0.3 | Drugs Databases Parser |
| dbplyr | 2.5.0 | A 'dplyr' Back End for Databases |
| dbscan | 1.1-12 | Density-Based Spatial Clustering of Applications with Noise (DBSCAN) and Related Algorithms |
| DDRTree | 0.1.5 | Learning Principal Graphs with DDRTree |
| decor | 1.0.2 | Retrieve Code Decorations |
| DelayedArray | 0.30.0 | A unified framework for working transparently with on-disk and in-memory array-like datasets |
| DelayedMatrixStats | 1.24.0 | Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects |
| deldir | 2.0-4 | Delaunay Triangulation and Dirichlet (Voronoi) Tessellation |
| dendextend | 1.17.1 | Extending 'dendrogram' Functionality in R |
| densityClust | 0.3.3 | Clustering by Fast Search and Find of Density Peaks |
| densvis | 1.12.1 | Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction |
| DEoptimR | 1.1-3 | Differential Evolution Optimization in Pure R |
| desc | 1.4.3 | Manipulate DESCRIPTION Files |
| DESeq2 | 1.42.1 | Differential gene expression analysis based on the negative binomial distribution |
| devtools | 2.4.5 | Tools to Make Developing R Packages Easier |
| diagram | 1.6.5 | Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams |
| DiagrammeR | 1.0.11 | Graph/Network Visualization |
| dials | 1.2.1 | Tools for Creating Tuning Parameter Values |
| DiceDesign | 1.10 | Designs of Computer Experiments |
| dichromat | 2.0-0.1 | Color Schemes for Dichromats |
| diffobj | 0.3.5 | Diffs for R Objects |
| digest | 0.6.35 | Create Compact Hash Digests of R Objects |
| dir.expiry | 1.10.0 | Managing Expiration for Cache Directories |
| DirichletMultinomial | 1.44.0 | Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data |
| distributional | 0.4.0 | Vectorised Probability Distributions |
| DNAcopy | 1.76.0 | DNA Copy Number Data Analysis |
| docopt | 0.7.1 | Command-Line Interface Specification Language |
| doFuture | 1.0.1 | Use Foreach to Parallelize via the Future Framework |
| doMC | 1.3.8 | Foreach Parallel Adaptor for 'parallel' |
| doParallel | 1.0.17 | Foreach Parallel Adaptor for the 'parallel' Package |
| doRNG | 1.8.6 | Generic Reproducible Parallel Backend for 'foreach' Loops |
| DOSE | 3.28.2 | Disease Ontology Semantic and Enrichment analysis |
| doSNOW | 1.0.20 | Foreach Parallel Adaptor for the 'snow' Package |
| dotCall64 | 1.1-1 | Enhanced Foreign Function Interface Supporting Long Vectors |
| downlit | 0.4.3 | Syntax Highlighting and Automatic Linking |
| downloader | 0.4 | Download Files over HTTP and HTTPS |
| dplyr | 1.1.4 | A Grammar of Data Manipulation |
| dqrng | 0.3.2 | Fast Pseudo Random Number Generators |
| DT | 0.33 | A Wrapper of the JavaScript Library 'DataTables' |
| dtplyr | 1.3.1 | Data Table Back-End for 'dplyr' |
| dygraphs | 1.1.1.6 | Interface to 'Dygraphs' Interactive Time Series Charting Library |
| dynamicTreeCut | 1.63-1 | Methods for Detection of Clusters in Hierarchical Clustering Dendrograms |
| e1071 | 1.7-14 | Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien |
| edgeR | 4.0.16 | Empirical Analysis of Digital Gene Expression Data in R |
| egg | 0.4.5 | Extensions for 'ggplot2': Custom Geom, Custom Themes, Plot Alignment, Labelled Panels, Symmetric Scales, and Fixed Panel Size |
| eigenmodel | 1.11 | Semiparametric Factor and Regression Models for Symmetric Relational Data |
| ellipse | 0.5.0 | Functions for Drawing Ellipses and Ellipse-Like Confidence Regions |
| ellipsis | 0.3.2 | Tools for Working with ... |
| emdbook | 1.3.13 | Support Functions and Data for "Ecological Models and Data" |
| emmeans | 1.10.1 | Estimated Marginal Means, aka Least-Squares Means |
| emoa | 0.5-2 | Evolutionary Multiobjective Optimization Algorithms |
| EnhancedVolcano | 1.20.0 | Publication-ready volcano plots with enhanced colouring and labeling |
| EnrichedHeatmap | 1.32.0 | Making Enriched Heatmaps |
| enrichplot | 1.22.0 | Visualization of Functional Enrichment Result |
| EnsDb.Hsapiens.v86 | 2.99.0 | Ensembl based annotation package |
| ensembldb | 2.26.0 | Utilities to create and use Ensembl-based annotation databases |
| EnvStats | 2.8.1 | Package for Environmental Statistics, Including US EPA Guidance |
| estimability | 1.5 | Tools for Assessing Estimability of Linear Predictions |
| etrunct | 0.1 | Computes Moments of Univariate Truncated t Distribution |
| eulerr | 7.0.2 | Area-Proportional Euler and Venn Diagrams with Ellipses |
| evaluate | 0.23 | Parsing and Evaluation Tools that Provide More Details than the Default |
| exactRankTests | 0.8-35 | Exact Distributions for Rank and Permutation Tests |
| ExperimentHub | 2.10.0 | Client to access ExperimentHub resources |
| expm | 0.999-9 | Matrix Exponential, Log, 'etc' |
| extrafont | 0.19 | Tools for Using Fonts |
| extrafontdb | 1.0 | Package for holding the database for the extrafont package |
| factoextra | 1.0.7 | Extract and Visualize the Results of Multivariate Data Analyses |
| FactoMineR | 2.11 | Multivariate Exploratory Data Analysis and Data Mining |
| fANCOVA | 0.6-1 | Nonparametric Analysis of Covariance |
| fansi | 1.0.6 | ANSI Control Sequence Aware String Functions |
| farver | 2.1.1 | High Performance Colour Space Manipulation |
| fastcluster | 1.2.6 | Fast Hierarchical Clustering Routines for R and 'Python' |
| fastDummies | 1.7.3 | Fast Creation of Dummy (Binary) Columns and Rows from Categorical Variables |
| fastICA | 1.2-4 | FastICA Algorithms to Perform ICA and Projection Pursuit |
| fastmap | 1.1.1 | Fast Data Structures |
| fastmatch | 1.1-4 | Fast 'match()' Function |
| fdrtool | 1.2.17 | Estimation of (Local) False Discovery Rates and Higher Criticism |
| feather | 0.3.5 | R Bindings to the Feather 'API' |
| ff | 4.0.12 | Memory-Efficient Storage of Large Data on Disk and Fast Access Functions |
| fftwtools | 0.9-11 | Wrapper for 'FFTW3' Includes: One-Dimensional, Two-Dimensional, Three-Dimensional, and Multivariate Transforms |
| fgsea | 1.28.0 | Fast Gene Set Enrichment Analysis |
| fields | 15.2 | Tools for Spatial Data |
| filelock | 1.0.3 | Portable File Locking |
| fitdistrplus | 1.1-11 | Help to Fit of a Parametric Distribution to Non-Censored or Censored Data |
| flashClust | 1.01-2 | Implementation of optimal hierarchical clustering |
| flextable | 0.9.6 | Functions for Tabular Reporting |
| fmsb | 0.7.6 | Functions for Medical Statistics Book with some Demographic Data |
| FNN | 1.1.4 | Fast Nearest Neighbor Search Algorithms and Applications |
| fontawesome | 0.5.2 | Easily Work with 'Font Awesome' Icons |
| fontBitstreamVera | 0.1.1 | Fonts with 'Bitstream Vera Fonts' License |
| fontLiberation | 0.1.0 | Liberation Fonts |
| fontquiver | 0.2.1 | Set of Installed Fonts |
| forcats | 1.0.0 | Tools for Working with Categorical Variables (Factors) |
| foreach | 1.5.2 | Provides Foreach Looping Construct |
| foreign | 0.8-86 | Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', 'dBase', ... |
| formatR | 1.14 | Format R Code Automatically |
| formattable | 0.2.1 | Create 'Formattable' Data Structures |
| Formula | 1.2-5 | Extended Model Formulas |
| formula.tools | 1.7.1 | Programmatic Utilities for Manipulating Formulas, Expressions, Calls, Assignments and Other R Objects |
| freesurferformats | 0.1.18 | Read and Write 'FreeSurfer' Neuroimaging File Formats |
| fresh | 0.2.0 | Create Custom 'Bootstrap' Themes to Use in 'Shiny' |
| fs | 1.6.4 | Cross-Platform File System Operations Based on 'libuv' |
| fsbrain | 0.5.5 | Managing and Visualizing Brain Surface Data |
| fslr | 2.25.2 | Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB') |
| furrr | 0.3.1 | Apply Mapping Functions in Parallel using Futures |
| futile.logger | 1.4.3 | A Logging Utility for R |
| futile.options | 1.0.1 | Futile Options Management |
| future | 1.33.2 | Unified Parallel and Distributed Processing in R for Everyone |
| future.apply | 1.11.2 | Apply Function to Elements in Parallel using Futures |
| gamm4 | 0.2-6 | Generalized Additive Mixed Models using 'mgcv' and 'lme4' |
| gargle | 1.5.2 | Utilities for Working with Google APIs |
| gbm | 2.1.9 | Generalized Boosted Regression Models |
| gclus | 1.3.2 | Clustering Graphics |
| gcrma | 2.74.0 | Background Adjustment Using Sequence Information |
| gdata | 3.0.0 | Various R Programming Tools for Data Manipulation |
| gdsfmt | 1.38.0 | R Interface to CoreArray Genomic Data Structure (GDS) Files |
| gdtools | 0.3.7 | Utilities for Graphical Rendering and Fonts Management |
| geeM | 0.10.1 | Solve Generalized Estimating Equations |
| geepack | 1.3.10 | Generalized Estimating Equation Package |
| genefilter | 1.84.0 | genefilter: methods for filtering genes from high-throughput experiments |
| geneplotter | 1.80.0 | Graphics related functions for Bioconductor |
| generics | 0.1.3 | Common S3 Generics not Provided by Base R Methods Related to Model Fitting |
| GENIE3 | 1.22.0 | GEne Network Inference with Ensemble of trees |
| genio | 1.1.2 | Genetics Input/Output Functions |
| GenomeInfoDb | 1.40.0 | Utilities for manipulating chromosome names, including modifying them to follow a particular naming style |
| GenomeInfoDbData | 1.2.12 | Species and taxonomy ID look up tables used by GenomeInfoDb |
| GenomicAlignments | 1.40.0 | Representation and manipulation of short genomic alignments |
| GenomicFeatures | 1.54.4 | Conveniently import and query gene models |
| GenomicRanges | 1.56.0 | Representation and manipulation of genomic intervals |
| GenSA | 1.1.14 | R Functions for Generalized Simulated Annealing |
| geojsonsf | 2.0.3 | GeoJSON to Simple Feature Converter |
| geometries | 0.2.4 | Convert Between R Objects and Geometric Structures |
| gert | 2.0.1 | Simple Git Client for R |
| getopt | 1.20.4 | C-Like 'getopt' Behavior |
| GetoptLong | 1.0.5 | Parsing Command-Line Arguments and Simple Variable Interpolation |
| gfonts | 0.2.0 | Offline 'Google' Fonts for 'Markdown' and 'Shiny' |
| ggalluvial | 0.12.5 | Alluvial Plots in 'ggplot2' |
| GGally | 2.2.1 | Extension to 'ggplot2' |
| ggbeeswarm | 0.7.2 | Categorical Scatter (Violin Point) Plots |
| ggbio | 1.50.0 | Visualization tools for genomic data |
| ggdist | 3.3.2 | Visualizations of Distributions and Uncertainty |
| ggforce | 0.4.2 | Accelerating 'ggplot2' |
| ggformula | 0.12.0 | Formula Interface to the Grammar of Graphics |
| ggfun | 0.1.4 | Miscellaneous Functions for 'ggplot2' |
| ggnetwork | 0.5.13 | Geometries to Plot Networks with 'ggplot2' |
| ggnewscale | 0.4.10 | Multiple Fill and Colour Scales in 'ggplot2' |
| ggplot2 | 3.5.1 | Create Elegant Data Visualisations Using the Grammar of Graphics |
| ggplotify | 0.1.2 | Convert Plot to 'grob' or 'ggplot' Object |
| ggpubr | 0.6.0 | 'ggplot2' Based Publication Ready Plots |
| ggraph | 2.2.1 | An Implementation of Grammar of Graphics for Graphs and Networks |
| ggrastr | 1.0.2 | Rasterize Layers for 'ggplot2' |
| ggrepel | 0.9.5 | Automatically Position Non-Overlapping Text Labels with 'ggplot2' |
| ggridges | 0.5.6 | Ridgeline Plots in 'ggplot2' |
| ggsci | 3.0.3 | Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2' |
| ggsignif | 0.6.4 | Significance Brackets for 'ggplot2' |
| ggstance | 0.3.7 | Horizontal 'ggplot2' Components |
| ggstats | 0.6.0 | Extension to 'ggplot2' for Plotting Stats |
| ggtext | 0.1.2 | Improved Text Rendering Support for 'ggplot2' |
| ggthemes | 5.1.0 | Extra Themes, Scales and Geoms for 'ggplot2' |
| ggtree | 3.10.1 | an R package for visualization of tree and annotation data |
| ggVennDiagram | 1.5.2 | A 'ggplot2' Implement of Venn Diagram |
| gh | 1.4.1 | 'GitHub' 'API' |
| gistr | 0.9.0 | Work with 'GitHub' 'Gists' |
| gitcreds | 0.1.2 | Query 'git' Credentials from 'R' |
| glasso | 1.11 | Graphical Lasso: Estimation of Gaussian Graphical Models |
| gld | 2.6.6 | Estimation and Use of the Generalised (Tukey) Lambda Distribution |
| glmmTMB | 1.1.9 | Generalized Linear Mixed Models using Template Model Builder |
| glmnet | 4.1-8 | Lasso and Elastic-Net Regularized Generalized Linear Models |
| GlobalOptions | 0.1.2 | Generate Functions to Get or Set Global Options |
| globals | 0.16.3 | Identify Global Objects in R Expressions |
| glue | 1.7.0 | Interpreted String Literals |
| GO.db | 3.18.0 | A set of annotation maps describing the entire Gene Ontology |
| goftest | 1.2-3 | Classical Goodness-of-Fit Tests for Univariate Distributions |
| googledrive | 2.1.1 | An Interface to Google Drive |
| googlesheets4 | 1.1.1 | Access Google Sheets using the Sheets API V4 |
| GOSemSim | 2.28.1 | GO-terms Semantic Similarity Measures |
| gower | 1.0.1 | Gower's Distance |
| GPfit | 1.0-8 | Gaussian Processes Modeling |
| gplots | 3.1.3.1 | Various R Programming Tools for Plotting Data |
| gprofiler2 | 0.2.3 | Interface to the 'g:Profiler' Toolset |
| graph | 1.82.0 | graph: A package to handle graph data structures |
| graphics | 4.4.0 | The R Graphics Package |
| graphite | 1.48.0 | GRAPH Interaction from pathway Topological Environment |
| graphlayouts | 1.1.1 | Additional Layout Algorithms for Network Visualizations |
| grDevices | 4.4.0 | The R Graphics Devices and Support for Colours and Fonts |
| grid | 4.4.0 | The Grid Graphics Package |
| gridBase | 0.4-7 | Integration of base and grid graphics |
| gridExtra | 2.3 | Miscellaneous Functions for "Grid" Graphics |
| gridGraphics | 0.5-1 | Redraw Base Graphics Using 'grid' Graphics |
| gridtext | 0.1.5 | Improved Text Rendering Support for 'Grid' Graphics |
| grr | 0.9.5 | Alternative Implementations of Base R Functions |
| GSA | 1.03.3 | Gene Set Analysis |
| GSEABase | 1.66.0 | Gene set enrichment data structures and methods |
| gson | 0.1.0 | Base Class and Methods for 'gson' Format |
| gstat | 2.1-1 | Spatial and Spatio-Temporal Geostatistical Modelling, Prediction and Simulation |
| gsubfn | 0.7 | Utilities for Strings and Function Arguments |
| GSVA | 1.52.0 | Gene Set Variation Analysis for Microarray and RNA-Seq Data |
| gt | 0.10.1 | Easily Create Presentation-Ready Display Tables |
| gtable | 0.3.5 | Arrange 'Grobs' in Tables |
| gtools | 3.9.5 | Various R Programming Tools |
| gtsummary | 1.7.2 | Presentation-Ready Data Summary and Analytic Result Tables |
| GWASExactHW | 1.2 | Exact Hardy-Weinburg Testing for Genome Wide Association Studies |
| GWASTools | 1.48.0 | Tools for Genome Wide Association Studies |
| gwasurvivr | 1.20.0 | gwasurvivr: an R package for genome wide survival analysis |
| h2o | 3.44.0.3 | R Interface for the 'H2O' Scalable Machine Learning Platform |
| hardhat | 1.3.1 | Construct Modeling Packages |
| harmony | 1.2.0 | Fast, Sensitive, and Accurate Integration of Single Cell Data |
| hash | 2.2.6.3 | Full Featured Implementation of Hash Tables/Associative Arrays/Dictionaries |
| haven | 2.5.4 | Import and Export 'SPSS', 'Stata' and 'SAS' Files |
| HDF5Array | 1.32.0 | HDF5 backend for DelayedArray objects |
| hdf5r | 1.3.10 | Interface to the 'HDF5' Binary Data Format |
| HDO.db | 0.99.1 | A set of annotation maps describing the entire Human Disease Ontology |
| heatmaply | 1.5.0 | Interactive Cluster Heat Maps Using 'plotly' and 'ggplot2' |
| heplots | 1.7.0 | Visualizing Hypothesis Tests in Multivariate Linear Models |
| here | 1.0.1 | A Simpler Way to Find Your Files |
| hexbin | 1.28.3 | Hexagonal Binning Routines |
| highr | 0.10 | Syntax Highlighting for R Source Code |
| Hmisc | 5.1-2 | Harrell Miscellaneous |
| hms | 1.1.3 | Pretty Time of Day |
| hrbrthemes | 0.8.7 | Additional Themes, Theme Components and Utilities for 'ggplot2' |
| HSMMSingleCell | 1.22.0 | Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM) |
| htmlTable | 2.4.2 | Advanced Tables for Markdown/HTML |
| htmltools | 0.5.8.1 | Tools for HTML |
| htmlwidgets | 1.6.4 | HTML Widgets for R |
| httpcode | 0.3.0 | 'HTTP' Status Code Helper |
| httpuv | 1.6.15 | HTTP and WebSocket Server Library |
| httr | 1.4.7 | Tools for Working with URLs and HTTP |
| httr2 | 1.0.1 | Perform HTTP Requests and Process the Responses |
| hwriter | 1.3.2.1 | HTML Writer - Outputs R Objects in HTML Format |
| ica | 1.0-3 | Independent Component Analysis |
| ids | 1.0.1 | Generate Random Identifiers |
| igraph | 2.0.3 | Network Analysis and Visualization |
| imager | 1.0.1 | Image Processing Library Based on 'CImg' |
| impute | 1.76.0 | impute: Imputation for microarray data |
| infer | 1.0.7 | Tidy Statistical Inference |
| influenceR | 0.1.5 | Software Tools to Quantify Structural Importance of Nodes in a Network |
| ini | 0.3.1 | Read and Write '.ini' Files |
| inline | 0.3.19 | Functions to Inline C, C++, Fortran Function Calls from R |
| insight | 0.19.10 | Easy Access to Model Information for Various Model Objects |
| interactiveDisplayBase | 1.40.0 | Base package for enabling powerful shiny web displays of Bioconductor objects |
| interp | 1.1-6 | Interpolation Methods |
| intervals | 0.15.4 | Tools for Working with Points and Intervals |
| invgamma | 1.1 | The Inverse Gamma Distribution |
| iotools | 0.3-5 | I/O Tools for Streaming |
| ipred | 0.9-14 | Improved Predictors |
| IRanges | 2.38.0 | Foundation of integer range manipulation in Bioconductor |
| IRdisplay | 1.1 | 'Jupyter' Display Machinery |
| IRkernel | 1.3.2 | Native R Kernel for the 'Jupyter Notebook' |
| irlba | 2.3.5.1 | Fast Truncated Singular Value Decomposition and Principal Components Analysis for Large Dense and Sparse Matrices |
| IsingFit | 0.4 | Fitting Ising Models Using the ELasso Method |
| IsingSampler | 0.2.3 | Sampling Methods and Distribution Functions for the Ising Model |
| isoband | 0.2.7 | Generate Isolines and Isobands from Regularly Spaced Elevation Grids |
| iterators | 1.0.14 | Provides Iterator Construct |
| ITKR | 0.6.0.0.2 | ITK in R |
| janitor | 2.2.0 | Simple Tools for Examining and Cleaning Dirty Data |
| jomo | 2.7-6 | Multilevel Joint Modelling Multiple Imputation |
| jpeg | 0.1-10 | Read and write JPEG images |
| jquerylib | 0.1.4 | Obtain 'jQuery' as an HTML Dependency Object |
| jsonify | 1.2.2 | Convert Between 'R' Objects and Javascript Object Notation (JSON) |
| jsonlite | 1.8.8 | A Simple and Robust JSON Parser and Generator for R |
| juicyjuice | 0.1.0 | Inline CSS Properties into HTML Tags Using 'juice' |
| kableExtra | 1.4.0 | Construct Complex Table with 'kable' and Pipe Syntax |
| KEGGgraph | 1.62.0 | KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor |
| KEGGREST | 1.44.0 | Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) |
| kernlab | 0.9-32 | Kernel-Based Machine Learning Lab |
| KernSmooth | 2.23-22 | Functions for Kernel Smoothing Supporting Wand & Jones (1995) |
| kinship2 | 1.9.6.1 | Pedigree Functions |
| km.ci | 0.5-6 | Confidence Intervals for the Kaplan-Meier Estimator |
| KMsurv | 0.1-5 | Data sets from Klein and Moeschberger (1997), Survival Analysis |
| knitr | 1.46 | A General-Purpose Package for Dynamic Report Generation in R |
| ks | 1.14.2 | Kernel Smoothing |
| kutils | 1.73 | Project Management Tools |
| labeling | 0.4.3 | Axis Labeling |
| labelled | 2.13.0 | Manipulating Labelled Data |
| laeken | 0.5.3 | Estimation of Indicators on Social Exclusion and Poverty |
| lambda.r | 1.2.4 | Modeling Data with Functional Programming |
| later | 1.3.2 | Utilities for Scheduling Functions to Execute Later with Event Loops |
| lattice | 0.22-6 | Trellis Graphics for R |
| latticeExtra | 0.6-30 | Extra Graphical Utilities Based on Lattice |
| lava | 1.8.0 | Latent Variable Models |
| lavaan | 0.6-17 | Latent Variable Analysis |
| lazyeval | 0.2.2 | Lazy (Non-Standard) Evaluation |
| leafem | 0.2.3 | 'leaflet' Extensions for 'mapview' |
| leaflet | 2.2.2 | Create Interactive Web Maps with the JavaScript 'Leaflet' Library |
| leaflet.providers | 2.0.0 | Leaflet Providers |
| leafpop | 0.1.0 | Include Tables, Images and Graphs in Leaflet Pop-Ups |
| leafsync | 0.1.0 | Small Multiples for Leaflet Web Maps |
| leaps | 3.1 | Regression Subset Selection |
| leiden | 0.4.3.1 | R Implementation of Leiden Clustering Algorithm |
| leidenbase | 0.1.27 | R and C/C++ Wrappers to Run the Leiden find_partition() Function |
| lhs | 1.1.6 | Latin Hypercube Samples |
| lifecycle | 1.0.4 | Manage the Life Cycle of your Package Functions |
| limma | 3.60.0 | Linear Models for Microarray Data |
| linkcomm | 1.0-14 | Tools for Generating, Visualizing, and Analysing Link Communities in Networks |
| lisrelToR | 0.3 | Import Output from LISREL into R |
| listenv | 0.9.1 | Environments Behaving (Almost) as Lists |
| lme4 | 1.1-35.3 | Linear Mixed-Effects Models using 'Eigen' and S4 |
| lmerTest | 3.1-3 | Tests in Linear Mixed Effects Models |
| lmom | 3.0 | L-Moments |
| lmtest | 0.9-40 | Testing Linear Regression Models |
| lobstr | 1.1.2 | Visualize R Data Structures with Trees |
| locfdr | 1.1-8 | Computes Local False Discovery Rates |
| locfit | 1.5-9.9 | Local Regression, Likelihood and Density Estimation |
| logistf | 1.26.0 | Firth's Bias-Reduced Logistic Regression |
| loo | 2.7.0 | Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models |
| lubridate | 1.9.3 | Make Dealing with Dates a Little Easier |
| lwgeom | 0.2-14 | Bindings to Selected 'liblwgeom' Functions for Simple Features |
| magick | 2.8.3 | Advanced Graphics and Image-Processing in R |
| magrittr | 2.0.3 | A Forward-Pipe Operator for R |
| manipulateWidget | 0.11.1 | Add Even More Interactivity to Interactive Charts |
| mapproj | 1.2.11 | Map Projections |
| maps | 3.4.2 | Draw Geographical Maps |
| mapview | 2.11.2 | Interactive Viewing of Spatial Data in R |
| marginaleffects | 0.20.0 | Predictions, Comparisons, Slopes, Marginal Means, and Hypothesis Tests |
| markdown | 1.12 | Render Markdown with 'commonmark' |
| MASS | 7.3-60.2 | Support Functions and Datasets for Venables and Ripley's MASS |
| mathjaxr | 1.6-0 | Using 'Mathjax' in Rd Files |
| Matrix | 1.7-0 | Sparse and Dense Matrix Classes and Methods |
| Matrix.utils | 0.9.7 | Data.frame-Like Operations on Sparse and Dense Matrix Objects |
| matrixcalc | 1.0-6 | Collection of Functions for Matrix Calculations |
| MatrixGenerics | 1.16.0 | S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects |
| MatrixModels | 0.5-3 | Modelling with Sparse and Dense Matrices |
| matrixStats | 1.3.0 | Functions that Apply to Rows and Columns of Matrices (and to Vectors) |
| maxLik | 1.5-2.1 | Maximum Likelihood Estimation and Related Tools |
| maxstat | 0.7-25 | Maximally Selected Rank Statistics |
| mbend | 1.3.1 | Matrix Bending |
| MCL | 1.0 | Markov Cluster Algorithm |
| mclogit | 0.9.6 | Multinomial Logit Models, with or without Random Effects or Overdispersion |
| mclust | 6.1.1 | Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation |
| memisc | 0.99.31.7 | Management of Survey Data and Presentation of Analysis Results |
| memoise | 2.0.1 | 'Memoisation' of Functions |
| MESS | 0.5.12 | Miscellaneous Esoteric Statistical Scripts |
| metadat | 1.2-0 | Meta-Analysis Datasets |
| metafor | 4.6-0 | Meta-Analysis Package for R |
| metapod | 1.10.1 | Meta-Analyses on P-Values of Differential Analyses |
| methods | 4.4.0 | Formal Methods and Classes |
| mgcv | 1.9-1 | Mixed GAM Computation Vehicle with Automatic Smoothness Estimation |
| mgm | 1.2-14 | Estimating Time-Varying k-Order Mixed Graphical Models |
| mi | 1.1 | Missing Data Imputation and Model Checking |
| mice | 3.16.0 | Multivariate Imputation by Chained Equations |
| mime | 0.12 | Map Filenames to MIME Types |
| miniUI | 0.1.1.1 | Shiny UI Widgets for Small Screens |
| minqa | 1.2.6 | Derivative-Free Optimization Algorithms by Quadratic Approximation |
| misc3d | 0.9-1 | Miscellaneous 3D Plots |
| miscTools | 0.6-28 | Miscellaneous Tools and Utilities |
| mitml | 0.4-5 | Tools for Multiple Imputation in Multilevel Modeling |
| mitools | 2.4 | Tools for Multiple Imputation of Missing Data |
| mixsqp | 0.3-54 | Sequential Quadratic Programming for Fast Maximum-Likelihood Estimation of Mixture Proportions |
| mixtools | 2.0.0 | Tools for Analyzing Finite Mixture Models |
| mlr | 2.19.1 | Machine Learning in R |
| mlrMBO | 1.1.5.1 | Bayesian Optimization and Model-Based Optimization of Expensive Black-Box Functions |
| mnormt | 2.1.1 | The Multivariate Normal and t Distributions, and Their Truncated Versions |
| modeldata | 1.3.0 | Data Sets Useful for Modeling Examples |
| modelenv | 0.1.1 | Provide Tools to Register Models for Use in 'tidymodels' |
| ModelMetrics | 1.2.2.2 | Rapid Calculation of Model Metrics |
| modelr | 0.1.11 | Modelling Functions that Work with the Pipe |
| monocle | 2.30.1 | Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq |
| monocle3 | 1.3.7 | Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq |
| mosaicCore | 0.9.4.0 | Common Utilities for Other MOSAIC-Family Packages |
| motifmatchr | 1.24.0 | Fast Motif Matching in R |
| msigdbr | 7.5.1 | MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format |
| multcomp | 1.4-25 | Simultaneous Inference in General Parametric Models |
| multcompView | 0.1-10 | Visualizations of Paired Comparisons |
| multicool | 1.0.1 | Permutations of Multisets in Cool-Lex Order |
| multicross | 2.1.0 | A Graph-Based Test for Comparing Multivariate Distributions in the Multi Sample Framework |
| multtest | 2.58.0 | Resampling-based multiple hypothesis testing |
| munsell | 0.5.1 | Utilities for Using Munsell Colours |
| muscat | 1.16.0 | Multi-sample multi-group scRNA-seq data analysis tools |
| mutoss | 0.1-13 | Unified Multiple Testing Procedures |
| mvtnorm | 1.2-4 | Multivariate Normal and t Distributions |
| nabor | 0.5.0 | Wraps 'libnabo', a Fast K Nearest Neighbour Library for Low Dimensions |
| nbpMatching | 1.5.4 | Functions for Optimal Non-Bipartite Matching |
| ncdf4 | 1.22 | Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files |
| network | 1.18.2 | Classes for Relational Data |
| NetworkComparisonTest | 2.2.2 | Statistical Comparison of Two Networks Based on Several Invariance Measures |
| networkD3 | 0.4 | D3 JavaScript Network Graphs from R |
| NetworkToolbox | 1.4.2 | Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis |
| networktools | 1.5.2 | Tools for Identifying Important Nodes in Networks |
| neurobase | 1.32.3 | 'Neuroconductor' Base Package with Helper Functions for 'nifti' Objects |
| nleqslv | 3.3.5 | Solve Systems of Nonlinear Equations |
| nlme | 3.1-164 | Linear and Nonlinear Mixed Effects Models |
| nloptr | 2.0.3 | R Interface to NLopt |
| NMF | 0.27 | Algorithms and Framework for Nonnegative Matrix Factorization (NMF) |
| nnet | 7.3-19 | Feed-Forward Neural Networks and Multinomial Log-Linear Models |
| nnls | 1.5 | The Lawson-Hanson Algorithm for Non-Negative Least Squares (NNLS) |
| nortest | 1.0-4 | Tests for Normality |
| numDeriv | 2016.8-1.1 | Accurate Numerical Derivatives |
| odbc | 1.4.2 | Connect to ODBC Compatible Databases (using the DBI Interface) |
| officer | 0.6.6 | Manipulation of Microsoft Word and PowerPoint Documents |
| oligo | 1.66.0 | Preprocessing tools for oligonucleotide arrays |
| oligoClasses | 1.64.0 | Classes for high-throughput arrays supported by oligo and crlmm |
| OpenMx | 2.21.11 | Extended Structural Equation Modelling |
| openssl | 2.1.2 | Toolkit for Encryption, Signatures and Certificates Based on OpenSSL |
| openxlsx | 4.2.5.2 | Read, Write and Edit xlsx Files |
| operator.tools | 1.6.3 | Utilities for Working with R's Operators |
| optimx | 2023-10.21 | Expanded Replacement and Extension of the 'optim' Function |
| optparse | 1.7.5 | Command Line Option Parser |
| orca | 1.1-2 | Computation of Graphlet Orbit Counts in Sparse Graphs |
| ordinal | 2023.12-4 | Regression Models for Ordinal Data |
| org.Hs.eg.db | 3.18.0 | Genome wide annotation for Human |
| org.Mm.eg.db | 3.18.0 | Genome wide annotation for Mouse |
| OrganismDbi | 1.44.0 | Software to enable the smooth interfacing of different database packages |
| oro.nifti | 0.11.4 | Rigorous - 'NIfTI' + 'ANALYZE' + 'AFNI' : Input / Output |
| orthopolynom | 1.0-6.1 | Collection of Functions for Orthogonal and Orthonormal Polynomials |
| outliers | 0.15 | Tests for Outliers |
| packrat | 0.9.2 | A Dependency Management System for Projects and their R Package Dependencies |
| pals | 1.8 | Color Palettes, Colormaps, and Tools to Evaluate Them |
| pan | 1.9 | Multiple Imputation for Multivariate Panel or Clustered Data |
| parallel | 4.4.0 | Support for Parallel Computation in R |
| parallelly | 1.37.1 | Enhancing the 'parallel' Package |
| parallelMap | 1.5.1 | Unified Interface to Parallelization Back-Ends |
| ParamHelpers | 1.14.1 | Helpers for Parameters in Black-Box Optimization, Tuning and Machine Learning |
| paran | 1.5.3 | Horn's Test of Principal Components/Factors |
| parsnip | 1.2.1 | A Common API to Modeling and Analysis Functions |
| patchwork | 1.2.0 | The Composer of Plots |
| pathview | 1.42.0 | a tool set for pathway based data integration and visualization |
| pbapply | 1.7-2 | Adding Progress Bar to '*apply' Functions |
| pbdZMQ | 0.3-11 | Programming with Big Data -- Interface to 'ZeroMQ' |
| pbivnorm | 0.6.0 | Vectorized Bivariate Normal CDF |
| pbkrtest | 0.5.2 | Parametric Bootstrap, Kenward-Roger and Satterthwaite Based Methods for Test in Mixed Models |
| pbmcapply | 1.5.1 | Tracking the Progress of Mc*pply with Progress Bar |
| pcaMethods | 1.94.0 | A collection of PCA methods |
| pdist | 1.2.1 | Partitioned Distance Function |
| permute | 0.9-7 | Functions for Generating Restricted Permutations of Data |
| pfamAnalyzeR | 1.2.0 | Identification of domain isotypes in pfam data |
| pheatmap | 1.0.12 | Pretty Heatmaps |
| phia | 0.3-1 | Post-Hoc Interaction Analysis |
| pillar | 1.9.0 | Coloured Formatting for Columns |
| pixmap | 0.4-13 | Bitmap Images / Pixel Maps |
| pkgbuild | 1.4.4 | Find Tools Needed to Build R Packages |
| pkgconfig | 2.0.3 | Private Configuration for 'R' Packages |
| pkgdown | 2.0.9 | Make Static HTML Documentation for a Package |
| pkgfilecache | 0.1.5 | Download and Manage Optional Package Data |
| pkgload | 1.3.4 | Simulate Package Installation and Attach |
| PKI | 0.1-12 | Public Key Infrastucture for R Based on the X.509 Standard |
| plink | 1.5-1 | IRT Separate Calibration Linking Methods |
| plogr | 0.2.0 | The 'plog' C++ Logging Library |
| plot3D | 1.4.1 | Plotting Multi-Dimensional Data |
| plotly | 4.10.4 | Create Interactive Web Graphics via 'plotly.js' |
| plotrix | 3.8-4 | Various Plotting Functions |
| plyr | 1.8.9 | Tools for Splitting, Applying and Combining Data |
| png | 0.1-8 | Read and write PNG images |
| polyclip | 1.10-6 | Polygon Clipping |
| polylabelr | 0.2.0 | Find the Pole of Inaccessibility (Visual Center) of a Polygon |
| polynom | 1.4-1 | A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations |
| posterior | 1.5.0 | Tools for Working with Posterior Distributions |
| poweRlaw | 0.80.0 | Analysis of Heavy Tailed Distributions |
| ppcor | 1.1 | Partial and Semi-Partial (Part) Correlation |
| pracma | 2.4.4 | Practical Numerical Math Functions |
| praise | 1.0.0 | Praise Users |
| preprocessCore | 1.64.0 | A collection of pre-processing functions |
| presto | 1.0.0 | Fast Functions for Differential Expression using Wilcox and AUC |
| prettyunits | 1.2.0 | Pretty, Human Readable Formatting of Quantities |
| pROC | 1.18.5 | Display and Analyze ROC Curves |
| processx | 3.8.4 | Execute and Control System Processes |
| prodlim | 2023.08.28 | Product-Limit Estimation for Censored Event History Analysis |
| profileplyr | 1.18.0 | Visualization and annotation of read signal over genomic ranges with profileplyr |
| profvis | 0.3.8 | Interactive Visualizations for Profiling R Code |
| progress | 1.2.3 | Terminal Progress Bars |
| progressr | 0.14.0 | An Inclusive, Unifying API for Progress Updates |
| promises | 1.3.0 | Abstractions for Promise-Based Asynchronous Programming |
| ProtGenerics | 1.34.0 | Generic infrastructure for Bioconductor mass spectrometry packages |
| proto | 1.0.0 | Prototype Object-Based Programming |
| proxy | 0.4-27 | Distance and Similarity Measures |
| pryr | 0.1.6 | Tools for Computing on the Language |
| ps | 1.7.6 | List, Query, Manipulate System Processes |
| pscl | 1.5.9 | Political Science Computational Laboratory |
| psych | 2.4.3 | Procedures for Psychological, Psychometric, and Personality Research |
| purrr | 1.0.2 | Functional Programming Tools |
| pwr | 1.3-0 | Basic Functions for Power Analysis |
| qap | 0.1-2 | Heuristics for the Quadratic Assignment Problem (QAP) |
| qdapRegex | 0.7.8 | Regular Expression Removal, Extraction, and Replacement Tools |
| qgraph | 1.9.8 | Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation |
| qqconf | 1.3.2 | Creates Simultaneous Testing Bands for QQ-Plots |
| qqman | 0.1.9 | Q-Q and Manhattan Plots for GWAS Data |
| quadprog | 1.5-8 | Functions to Solve Quadratic Programming Problems |
| quantreg | 5.97 | Quantile Regression |
| quantsmooth | 1.68.0 | Quantile smoothing and genomic visualization of array data |
| questionr | 0.7.8 | Functions to Make Surveys Processing Easier |
| QuickJSR | 1.1.3 | Interface for the 'QuickJS' Lightweight 'JavaScript' Engine |
| qvalue | 2.34.0 | Q-value estimation for false discovery rate control |
| R.cache | 0.16.0 | Fast and Light-Weight Caching (Memoization) of Objects and Results to Speed Up Computations |
| R.matlab | 3.7.0 | Read and Write MAT Files and Call MATLAB from Within R |
| R.methodsS3 | 1.8.2 | S3 Methods Simplified |
| R.oo | 1.26.0 | R Object-Oriented Programming with or without References |
| R.utils | 2.12.3 | Various Programming Utilities |
| R2HTML | 2.3.3 | HTML Exportation for R Objects |
| R6 | 2.5.1 | Encapsulated Classes with Reference Semantics |
| ragg | 1.3.1 | Graphic Devices Based on AGG |
| randomForest | 4.7-1.1 | Breiman and Cutler's Random Forests for Classification and Regression |
| randomForestSRC | 3.2.3 | Fast Unified Random Forests for Survival, Regression, and Classification (RF-SRC) |
| ranger | 0.16.0 | A Fast Implementation of Random Forests |
| RANN | 2.6.1 | Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric |
| rapidjsonr | 1.2.0 | 'Rapidjson' C++ Header Files |
| rappdirs | 0.3.3 | Application Directories: Determine Where to Save Data, Caches, and Logs |
| raster | 3.6-26 | Geographic Data Analysis and Modeling |
| RBGL | 1.78.0 | An interface to the BOOST graph library |
| rbibutils | 2.2.16 | Read 'Bibtex' Files and Convert Between Bibliography Formats |
| RcisTarget | 1.22.0 | RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions |
| rcmdcheck | 1.4.0 | Run 'R CMD check' from 'R' and Capture Results |
| RColorBrewer | 1.1-3 | ColorBrewer Palettes |
| Rcpp | 1.0.12 | Seamless R and C++ Integration |
| RcppAnnoy | 0.0.22 | 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest Neighbors |
| RcppArmadillo | 0.12.8.2.1 | 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library |
| RcppEigen | 0.3.4.0.0 | 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library |
| RcppGSL | 0.3.13 | 'Rcpp' Integration for 'GNU GSL' Vectors and Matrices |
| RcppHNSW | 0.6.0 | 'Rcpp' Bindings for 'hnswlib', a Library for Approximate Nearest Neighbors |
| RcppML | 0.3.7 | Rcpp Machine Learning Library |
| RcppNumerical | 0.6-0 | 'Rcpp' Integration for Numerical Computing Libraries |
| RcppParallel | 5.1.7 | Parallel Programming Tools for 'Rcpp' |
| RcppProgress | 0.4.2 | An Interruptible Progress Bar with OpenMP Support for C++ in R Packages |
| RcppTOML | 0.2.2 | 'Rcpp' Bindings to Parser for "Tom's Obvious Markup Language" |
| RCurl | 1.98-1.14 | General Network (HTTP/FTP/...) Client Interface for R |
| RCy3 | 2.22.1 | Functions to Access and Control Cytoscape |
| Rdpack | 2.6 | Update and Manipulate Rd Documentation Objects |
| reactable | 0.4.4 | Interactive Data Tables for R |
| reactome.db | 1.86.2 | A set of annotation maps for reactome |
| ReactomePA | 1.46.0 | Reactome Pathway Analysis |
| reactR | 0.5.0 | React Helpers |
| readbitmap | 0.1.5 | Simple Unified Interface to Read Bitmap Images (BMP,JPEG,PNG,TIFF) |
| readr | 2.1.5 | Read Rectangular Text Data |
| readxl | 1.4.3 | Read Excel Files |
| recipes | 1.0.10 | Preprocessing and Feature Engineering Steps for Modeling |
| registry | 0.5-1 | Infrastructure for R Package Registries |
| remaCor | 0.0.18 | Random Effects Meta-Analysis for Correlated Test Statistics |
| rematch | 2.0.0 | Match Regular Expressions with a Nicer 'API' |
| rematch2 | 2.1.2 | Tidy Output from Regular Expression Matching |
| remotes | 2.5.0 | R Package Installation from Remote Repositories, Including 'GitHub' |
| renv | 1.0.7 | Project Environments |
| repr | 1.1.7 | Serializable Representations |
| reprex | 2.1.0 | Prepare Reproducible Example Code via the Clipboard |
| reshape | 0.8.9 | Flexibly Reshape Data |
| reshape2 | 1.4.4 | Flexibly Reshape Data: A Reboot of the Reshape Package |
| ResidualMatrix | 1.12.0 | Creating a DelayedMatrix of Regression Residuals |
| restfulr | 0.0.15 | R Interface to RESTful Web Services |
| reticulate | 1.36.1 | Interface to 'Python' |
| rex | 1.2.1 | Friendly Regular Expressions |
| rgl | 1.3.1 | 3D Visualization Using OpenGL |
| Rgraphviz | 2.46.0 | Provides plotting capabilities for R graph objects |
| rGREAT | 2.4.0 | GREAT Analysis - Functional Enrichment on Genomic Regions |
| rhdf5 | 2.48.0 | R Interface to HDF5 |
| rhdf5filters | 1.16.0 | HDF5 Compression Filters |
| Rhdf5lib | 1.26.0 | hdf5 library as an R package |
| RhpcBLASctl | 0.23-42 | Control the Number of Threads on 'BLAS' |
| Rhtslib | 3.0.0 | HTSlib high-throughput sequencing library as an R package |
| RInside | 0.2.18 | C++ Classes to Embed R in C++ (and C) Applications |
| rintrojs | 0.3.4 | Wrapper for the 'Intro.js' Library |
| rio | 1.0.1 | A Swiss-Army Knife for Data I/O |
| RITAN | 1.26.0 | Rapid Integration of Term Annotation and Network resources |
| RITANdata | 1.26.0 | This package contains reference annotation and network data sets |
| rJava | 1.0-11 | Low-Level R to Java Interface |
| rjson | 0.2.21 | JSON for R |
| RJSONIO | 1.3-1.9 | Serialize R Objects to JSON, JavaScript Object Notation |
| rlang | 1.1.3 | Functions for Base Types and Core R and 'Tidyverse' Features |
| rlist | 0.4.6.2 | A Toolbox for Non-Tabular Data Manipulation |
| RMariaDB | 1.3.1 | Database Interface and MariaDB Driver |
| rmarkdown | 2.26 | Dynamic Documents for R |
| Rmpi | 0.7-2 | Interface (Wrapper) to MPI (Message-Passing Interface) |
| Rnanoflann | 0.0.2 | Extremely Fast Nearest Neighbor Search |
| rngtools | 1.5.2 | Utility Functions for Working with Random Number Generators |
| RNifti | 1.6.1 | Fast R and C++ Access to NIfTI Images |
| robustbase | 0.99-2 | Basic Robust Statistics |
| rockchalk | 1.8.157 | Regression Estimation and Presentation |
| ROCR | 1.0-11 | Visualizing the Performance of Scoring Classifiers |
| rootSolve | 1.8.2.4 | Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations |
| ROpenCVLite | 4.90.1 | Helper Package for Installing OpenCV with R |
| roxygen2 | 7.3.1 | In-Line Documentation for R |
| rpart | 4.1.23 | Recursive Partitioning and Regression Trees |
| rpf | 1.0.14 | Response Probability Functions |
| RPresto | 1.4.6 | DBI Connector to Presto |
| rprojroot | 2.0.4 | Finding Files in Project Subdirectories |
| rsample | 1.2.1 | General Resampling Infrastructure |
| Rsamtools | 2.20.0 | Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import |
| rsconnect | 1.2.2 | Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io', and 'RPubs' |
| RSpectra | 0.16-1 | Solvers for Large-Scale Eigenvalue and SVD Problems |
| RSQLite | 2.3.6 | SQLite Interface for R |
| rstan | 2.32.6 | R Interface to Stan |
| rstantools | 2.4.0 | Tools for Developing R Packages Interfacing with 'Stan' |
| rstatix | 0.7.2 | Pipe-Friendly Framework for Basic Statistical Tests |
| rstudioapi | 0.16.0 | Safely Access the RStudio API |
| Rsubread | 2.16.1 | Mapping, quantification and variant analysis of sequencing data |
| rsvd | 1.0.5 | Randomized Singular Value Decomposition |
| rtracklayer | 1.62.0 | R interface to genome annotation files and the UCSC genome browser |
| Rtsne | 0.17 | T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation |
| Rttf2pt1 | 1.3.12 | 'ttf2pt1' Program |
| RUnit | 0.4.33 | R Unit Test Framework |
| rvcheck | 0.2.1 | R/Package Version Check |
| RVenn | 1.1.0 | Set Operations for Many Sets |
| rversions | 2.1.2 | Query 'R' Versions, Including 'r-release' and 'r-oldrel' |
| rvest | 1.0.4 | Easily Harvest (Scrape) Web Pages |
| s2 | 1.1.6 | Spherical Geometry Operators Using the S2 Geometry Library |
| S4Arrays | 1.4.0 | Foundation of array-like containers in Bioconductor |
| S4Vectors | 0.42.0 | Foundation of vector-like and list-like containers in Bioconductor |
| safetensors | 0.1.2 | Safetensors File Format |
| samr | 3.0 | SAM: Significance Analysis of Microarrays |
| sandwich | 3.1-0 | Robust Covariance Matrix Estimators |
| sass | 0.4.9 | Syntactically Awesome Style Sheets ('Sass') |
| satellite | 1.0.5 | Handling and Manipulating Remote Sensing Data |
| satuRn | 1.10.0 | Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications |
| ScaledMatrix | 1.12.0 | Creating a DelayedMatrix of Scaled and Centered Values |
| scales | 1.3.0 | Scale Functions for Visualization |
| scater | 1.30.1 | Single-Cell Analysis Toolkit for Gene Expression Data in R |
| scattermore | 1.2 | Scatterplots with More Points |
| scatterpie | 0.2.2 | Scatter Pie Plot |
| scatterplot3d | 0.3-44 | 3D Scatter Plot |
| SCENIC | 1.3.1 | SCENIC (Single Cell rEgulatory Network Inference and Clustering) |
| SCopeLoomR | 0.13.0 | Build .loom files (compatible with SCope) and extract data from .loom files. |
| SCPA | 1.6.1 | Single Cell Pathway Analysis |
| sctransform | 0.4.1 | Variance Stabilizing Transformations for Single Cell UMI Data |
| scuttle | 1.12.0 | Single-Cell RNA-Seq Analysis Utilities |
| segmented | 2.0-4 | Regression Models with Break-Points / Change-Points Estimation (with Possibly Random Effects) |
| selectr | 0.4-2 | Translate CSS Selectors to XPath Expressions |
| sem | 3.1-15 | Structural Equation Models |
| semPlot | 1.1.6 | Path Diagrams and Visual Analysis of Various SEM Packages' Output |
| sendmailR | 1.4-0 | Send Email Using R |
| seqinr | 4.2-36 | Biological Sequences Retrieval and Analysis |
| seqLogo | 1.68.0 | Sequence logos for DNA sequence alignments |
| seqminer | 9.4 | Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R |
| seriation | 1.5.5 | Infrastructure for Ordering Objects Using Seriation |
| servr | 0.30 | A Simple HTTP Server to Serve Static Files or Dynamic Documents |
| sessioninfo | 1.2.2 | R Session Information |
| Seurat | 5.0.3 | Tools for Single Cell Genomics |
| SeuratDisk | 0.0.0.9021 | Interfaces for HDF5-Based Single Cell File Formats |
| SeuratObject | 5.0.1 | Data Structures for Single Cell Data |
| SeuratWrappers | 0.3.5 | Community-Provided Methods and Extensions for the Seurat Object |
| sf | 1.0-16 | Simple Features for R |
| sfheaders | 0.4.4 | Converts Between R Objects and Simple Feature Objects |
| sftime | 0.2-0 | Classes and Methods for Simple Feature Objects that Have a Time Column |
| shadowtext | 0.1.3 | Shadow Text Grob and Layer |
| shape | 1.4.6.1 | Functions for Plotting Graphical Shapes, Colors |
| shiny | 1.8.1.1 | Web Application Framework for R |
| shinyAce | 0.4.2 | Ace Editor Bindings for Shiny |
| shinycssloaders | 1.0.0 | Add Loading Animations to a 'shiny' Output While It's Recalculating |
| shinydashboard | 0.7.2 | Create Dashboards with 'Shiny' |
| shinyFiles | 0.9.3 | A Server-Side File System Viewer for Shiny |
| shinyjs | 2.1.0 | Easily Improve the User Experience of Your Shiny Apps in Seconds |
| shinystan | 2.6.0 | Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models |
| shinythemes | 1.2.0 | Themes for Shiny |
| shinyWidgets | 0.8.6 | Custom Inputs Widgets for Shiny |
| ShortRead | 1.60.0 | FASTQ input and manipulation |
| simdistr | 1.0.1 | Assessment of Data Trial Distributions According to the Carlisle-Stouffer Method |
| SingleCellExperiment | 1.26.0 | S4 Classes for Single Cell Data |
| SingleR | 2.4.1 | Reference-Based Single-Cell RNA-Seq Annotation |
| singscore | 1.24.0 | Rank-based single-sample gene set scoring method |
| sitmo | 2.0.2 | Parallel Pseudo Random Number Generator (PPRNG) 'sitmo' Header Files |
| SKAT | 2.2.5 | SNP-Set (Sequence) Kernel Association Test |
| slam | 0.1-50 | Sparse Lightweight Arrays and Matrices |
| slider | 0.3.1 | Sliding Window Functions |
| smacof | 2.1-6 | Multidimensional Scaling |
| smoof | 1.6.0.3 | Single and Multi-Objective Optimization Test Functions |
| sn | 2.1.1 | The Skew-Normal and Related Distributions Such as the Skew-t and the SUN |
| sna | 2.7-2 | Tools for Social Network Analysis |
| snakecase | 0.11.1 | Convert Strings into any Case |
| snow | 0.4-4 | Simple Network of Workstations |
| SNPRelate | 1.36.1 | Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data |
| soGGi | 1.34.0 | Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals |
| sourcetools | 0.1.7-1 | Tools for Reading, Tokenizing and Parsing R Code |
| sp | 2.1-4 | Classes and Methods for Spatial Data |
| spacetime | 1.3-1 | Classes and Methods for Spatio-Temporal Data |
| spam | 2.10-0 | SPArse Matrix |
| SparseArray | 1.4.0 | High-performance sparse data representation and manipulation in R |
| SparseM | 1.81 | Sparse Linear Algebra |
| sparseMatrixStats | 1.16.0 | Summary Statistics for Rows and Columns of Sparse Matrices |
| sparsesvd | 0.2-2 | Sparse Truncated Singular Value Decomposition (from 'SVDLIBC') |
| SPAtest | 3.1.2 | Score Test and Meta-Analysis Based on Saddlepoint Approximation |
| spatial | 7.3-17 | Functions for Kriging and Point Pattern Analysis |
| SpatialExperiment | 1.14.0 | S4 Class for Spatially Resolved -omics Data |
| spatstat | 3.0-8 | Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests |
| spatstat.data | 3.0-4 | Datasets for 'spatstat' Family |
| spatstat.explore | 3.2-7 | Exploratory Data Analysis for the 'spatstat' Family |
| spatstat.geom | 3.2-9 | Geometrical Functionality of the 'spatstat' Family |
| spatstat.linnet | 3.1-5 | Linear Networks Functionality of the 'spatstat' Family |
| spatstat.model | 3.2-11 | Parametric Statistical Modelling and Inference for the 'spatstat' Family |
| spatstat.random | 3.2-3 | Random Generation Functionality for the 'spatstat' Family |
| spatstat.sparse | 3.0-3 | Sparse Three-Dimensional Arrays and Linear Algebra Utilities |
| spatstat.utils | 3.0-4 | Utility Functions for 'spatstat' |
| spData | 2.3.0 | Datasets for Spatial Analysis |
| spdep | 1.3-3 | Spatial Dependence: Weighting Schemes, Statistics |
| speedglm | 0.3-5 | Fitting Linear and Generalized Linear Models to Large Data Sets |
| splines | 4.4.0 | Regression Spline Functions and Classes |
| sqldf | 0.4-11 | Manipulate R Data Frames Using SQL |
| SQUAREM | 2021.1 | Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms |
| squash | 1.0.9 | Color-Based Plots for Multivariate Visualization |
| StanHeaders | 2.32.7 | C++ Header Files for Stan |
| stapler | 0.7.1 | Simultaneous Truth and Performance Level Estimation |
| stars | 0.6-5 | Spatiotemporal Arrays, Raster and Vector Data Cubes |
| statmod | 1.5.0 | Statistical Modeling |
| statnet.common | 4.9.0 | Common R Scripts and Utilities Used by the Statnet Project Software |
| stats | 4.4.0 | The R Stats Package |
| stats4 | 4.4.0 | Statistical Functions using S4 Classes |
| STRINGdb | 2.14.3 | STRINGdb - Protein-Protein Interaction Networks and Functional Enrichment Analysis |
| stringdist | 0.9.12 | Approximate String Matching, Fuzzy Text Search, and String Distance Functions |
| stringi | 1.8.4 | Fast and Portable Character String Processing Facilities |
| stringr | 1.5.1 | Simple, Consistent Wrappers for Common String Operations |
| StructuralVariantAnnotation | 1.18.0 | Variant annotations for structural variants |
| styler | 1.10.3 | Non-Invasive Pretty Printing of R Code |
| SummarizedExperiment | 1.34.0 | SummarizedExperiment container |
| survey | 4.4-2 | Analysis of Complex Survey Samples |
| survival | 3.6-4 | Survival Analysis |
| survminer | 0.4.9 | Drawing Survival Curves using 'ggplot2' |
| survMisc | 0.5.6 | Miscellaneous Functions for Survival Data |
| sva | 3.50.0 | Surrogate Variable Analysis |
| svglite | 2.1.3 | An 'SVG' Graphics Device |
| svUnit | 1.0.6 | 'SciViews' - Unit, Integration and System Testing |
| sys | 3.4.2 | Powerful and Reliable Tools for Running System Commands in R |
| systemfonts | 1.0.6 | System Native Font Finding |
| systemPipeR | 2.8.0 | systemPipeR: workflow management and report generation environment |
| tcltk | 4.4.0 | Tcl/Tk Interface |
| tensor | 1.5 | Tensor product of arrays |
| tensorA | 0.36.2.1 | Advanced Tensor Arithmetic with Named Indices |
| terra | 1.7-71 | Spatial Data Analysis |
| testthat | 3.2.1.1 | Unit Testing for R |
| textshaping | 0.3.7 | Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text Shaping |
| TFBSTools | 1.40.0 | Software Package for Transcription Factor Binding Site (TFBS) Analysis |
| TFisher | 0.2.0 | Optimal Thresholding Fisher's P-Value Combination Method |
| TFMPvalue | 0.0.9 | Efficient and Accurate P-Value Computation for Position Weight Matrices |
| TH.data | 1.1-2 | TH's Data Archive |
| threejs | 0.3.3 | Interactive 3D Scatter Plots, Networks and Globes |
| tibble | 3.2.1 | Simple Data Frames |
| tidybayes | 3.0.6 | Tidy Data and 'Geoms' for Bayesian Models |
| tidycmprsk | 1.0.0 | Competing Risks Estimation |
| tidygraph | 1.3.1 | A Tidy API for Graph Manipulation |
| tidymodels | 1.2.0 | Easily Install and Load the 'Tidymodels' Packages |
| tidyr | 1.3.1 | Tidy Messy Data |
| tidyselect | 1.2.1 | Select from a Set of Strings |
| tidytree | 0.4.6 | A Tidy Tool for Phylogenetic Tree Data Manipulation |
| tidyverse | 2.0.0 | Easily Install and Load the 'Tidyverse' |
| tiff | 0.1-12 | Read and Write TIFF Images |
| timechange | 0.3.0 | Efficient Manipulation of Date-Times |
| timeDate | 4032.109 | Rmetrics - Chronological and Calendar Objects |
| tinytex | 0.51 | Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents |
| tippy | 0.1.0 | Add Tooltips to 'R markdown' Documents or 'Shiny' Apps |
| tmap | 3.3-4 | Thematic Maps |
| tmaptools | 3.1-1 | Thematic Map Tools |
| TMB | 1.9.11 | Template Model Builder: A General Random Effect Tool Inspired by 'ADMB' |
| tmvnsim | 1.0-2 | Truncated Multivariate Normal Simulation |
| tools | 4.4.0 | Tools for Package Development |
| topGO | 2.54.0 | Enrichment Analysis for Gene Ontology |
| torch | 0.12.0 | Tensors and Neural Networks with 'GPU' Acceleration |
| treeio | 1.26.0 | Base Classes and Functions for Phylogenetic Tree Input and Output |
| triebeard | 0.4.1 | 'Radix' Trees in 'Rcpp' |
| truncnorm | 1.0-9 | Truncated Normal Distribution |
| TSP | 1.2-4 | Traveling Salesperson Problem (TSP) |
| tune | 1.2.1 | Tidy Tuning Tools |
| twang | 2.6 | Toolkit for Weighting and Analysis of Nonequivalent Groups |
| tweenr | 2.0.3 | Interpolate Data for Smooth Animations |
| TxDb.Hsapiens.UCSC.hg19.knownGene | 3.2.2 | Annotation package for TxDb object(s) |
| TxDb.Hsapiens.UCSC.hg38.knownGene | 3.18.0 | Annotation package for TxDb object(s) |
| TxDb.Mmusculus.UCSC.mm10.knownGene | 3.10.0 | Annotation package for TxDb object(s) |
| TxDb.Mmusculus.UCSC.mm9.knownGene | 3.2.2 | Annotation package for TxDb object(s) |
| tximeta | 1.20.3 | Transcript Quantification Import with Automatic Metadata |
| tximport | 1.30.0 | Import and summarize transcript-level estimates for transcript- and gene-level analysis |
| tzdb | 0.4.0 | Time Zone Database Information |
| ucminf | 1.2.1 | General-Purpose Unconstrained Non-Linear Optimization |
| UCSC.utils | 1.0.0 | Low-level utilities to retrieve data from the UCSC Genome Browser |
| UCSCXenaTools | 1.4.8 | Download and Explore Datasets from UCSC Xena Data Hubs |
| umap | 0.2.10.0 | Uniform Manifold Approximation and Projection |
| UniprotR | 2.4.0 | Retrieving Information of Proteins from Uniprot |
| units | 0.8-5 | Measurement Units for R Vectors |
| UpSetR | 1.4.0 | A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets |
| urlchecker | 1.0.1 | Run CRAN URL Checks from Older R Versions |
| urltools | 1.7.3 | Vectorised Tools for URL Handling and Parsing |
| useful | 1.2.6.1 | A Collection of Handy, Useful Functions |
| usethis | 2.2.3 | Automate Package and Project Setup |
| utf8 | 1.2.4 | Unicode Text Processing |
| utils | 4.4.0 | The R Utils Package |
| uuid | 1.2-0 | Tools for Generating and Handling of UUIDs |
| uwot | 0.2.2 | The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction |
| V8 | 4.4.2 | Embedded JavaScript and WebAssembly Engine for R |
| variables | 1.1-1 | Variable Descriptions |
| variancePartition | 1.32.5 | Quantify and interpret drivers of variation in multilevel gene expression experiments |
| VariantAnnotation | 1.48.1 | Annotation of Genetic Variants |
| vcd | 1.4-12 | Visualizing Categorical Data |
| vctrs | 0.6.5 | Vector Helpers |
| vegan | 2.6-4 | Community Ecology Package |
| venn | 1.12 | Draw Venn Diagrams |
| VennDiagram | 1.7.3 | Generate High-Resolution Venn and Euler Plots |
| VGAM | 1.1-10 | Vector Generalized Linear and Additive Models |
| VIM | 6.2.2 | Visualization and Imputation of Missing Values |
| vipor | 0.4.7 | Plot Categorical Data Using Quasirandom Noise and Density Estimates |
| viridis | 0.6.5 | Colorblind-Friendly Color Maps for R |
| viridisLite | 0.4.2 | Colorblind-Friendly Color Maps (Lite Version) |
| visNetwork | 2.1.2 | Network Visualization using 'vis.js' Library |
| vroom | 1.6.5 | Read and Write Rectangular Text Data Quickly |
| vsn | 3.70.0 | Variance stabilization and calibration for microarray data |
| waiter | 0.2.5 | Loading Screen for 'Shiny' |
| waldo | 0.5.2 | Find Differences Between R Objects |
| warp | 0.2.1 | Group Dates |
| webshot | 0.5.5 | Take Screenshots of Web Pages |
| weights | 1.0.4 | Weighting and Weighted Statistics |
| WGCNA | 1.72-5 | Weighted Correlation Network Analysis |
| whisker | 0.4.1 | {{mustache}} for R, Logicless Templating |
| WhiteStripe | 2.4.2 | White Matter Normalization for Magnetic Resonance Images |
| widgetframe | 0.3.1 | 'Htmlwidgets' in Responsive 'iframes' |
| withr | 3.0.0 | Run Code 'With' Temporarily Modified Global State |
| wk | 0.9.1 | Lightweight Well-Known Geometry Parsing |
| wordcloud | 2.6 | Word Clouds |
| workflows | 1.1.4 | Modeling Workflows |
| workflowsets | 1.1.0 | Create a Collection of 'tidymodels' Workflows |
| writexl | 1.5.0 | Export Data Frames to Excel 'xlsx' Format |
| xfun | 0.43 | Supporting Functions for Packages Maintained by 'Yihui Xie' |
| xgboost | 1.7.7.1 | Extreme Gradient Boosting |
| xlsx | 0.6.5 | Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Files |
| xlsxjars | 0.6.1 | Package required POI jars for the xlsx package |
| XML | 3.99-0.16.1 | Tools for Parsing and Generating XML Within R and S-Plus |
| xml2 | 1.3.6 | Parse XML |
| xopen | 1.0.1 | Open System Files, 'URLs', Anything |
| xtable | 1.8-4 | Export Tables to LaTeX or HTML |
| xts | 0.13.2 | eXtensible Time Series |
| XVector | 0.44.0 | Foundation of external vector representation and manipulation in Bioconductor |
| yaml | 2.3.8 | Methods to Convert R Data to YAML and Back |
| yardstick | 1.3.1 | Tidy Characterizations of Model Performance |
| yulab.utils | 0.1.4 | Supporting Functions for Packages Maintained by 'YuLab-SMU' |
| zip | 2.3.1 | Cross-Platform 'zip' Compression |
| zlibbioc | 1.50.0 | An R packaged zlib-1.2.5 |
| zoo | 1.8-12 | S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations) |