R libraries

 abind                   Combine multi-dimensional arrays
 aCGH                    Classes and functions for Array Comparative
                         Genomic Hybridization data.
 ade4                    Analysis of Ecological Data : Exploratory and
                         Euclidean methods in Environmental sciences
 affxparser              Affymetrix File Parsing SDK
 affy                    Methods for Affymetrix Oligonucleotide Arrays
 affydata                Affymetrix Data for Demonstration Purpose
 affyio                  Tools for parsing Affymetrix data files
 affyPLM                 Methods for fitting probe-level models
 affyQCReport            QC Report Generation for affyBatch objects
 Agi4x44PreProcess       PreProcessing of Agilent 4x44 array data
 agricolae               Statistical Procedures for Agricultural
                         Research
 akima                   Interpolation of irregularly spaced data
 annaffy                 Annotation tools for Affymetrix biological
                         metadata
 annotate                Annotation for microarrays
 AnnotationDbi           Annotation Database Interface
 AnnotationForge         Code for Building Annotation Database Packages
 ape                     Analyses of Phylogenetics and Evolution
 aplpack                 Another Plot PACKage: stem.leaf, bagplot,
                         faces, spin3R, and some slider functions
 aroma.affymetrix        Analysis of large Affymetrix microarray data
                         sets
 aroma.apd               A probe-level data file format used by
                         aroma.affymetrix [DEPRECATED]
 aroma.core              Core methods and classes used by aroma.*
                         packages part of The Aroma Framework
 aroma.light             Light-weight methods for normalization and
                         visualization of microarray data using only
                         basic R data types
 arrayQualityMetrics     Quality metrics on microarray data sets
 auteur                  Bayesian sampler of the trait-evolutionary
                         process
 aws                     Adaptive Weights Smoothing
 awsMethods              Class and Methods definitions for packages aws,
                         adimpro, fmri, dwi
 BAMD                    Bayesian Association Model for Genomic Data
                         with Missing Covariates
 base                    The R Base Package
 baySeq                  Empirical Bayesian analysis of patterns of
                         differential expression in count data
 beadarray               Quality assessment and low-level analysis for
                         Illumina BeadArray data
 BeadDataPackR           Compression of Illumina BeadArray data
 binom                   Binomial Confidence Intervals For Several
                         Parameterizations
 Biobase                 Biobase: Base functions for Bioconductor
 BiocGenerics            Generic functions for Bioconductor
 BiocInstaller           Install/Update Bioconductor and CRAN Packages
 biomaRt                 Interface to BioMart databases (e.g. Ensembl,
                         COSMIC ,Wormbase and Gramene)
 biomod2                 Ensemble platform for species distribution
                         modeling
 Biostrings              String objects representing biological
                         sequences, and matching algorithms
 biovizBase              Basic graphic utilities for visualization of
                         genomic data.
 bit                     A class for vectors of 1-bit booleans
 bitops                  Bitwise Operations
 boot                    Bootstrap Functions (originally by Angelo Canty
                         for S)
 BSgenome                Infrastructure for Biostrings-based genome data
                         packages
 Cairo                   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.
 car                     Companion to Applied Regression
 Category                Category Analysis
 caTools                 Tools: moving window statistics, GIF, Base64,
                         ROC AUC, etc.
 ce25bmrv02cdf           ce25bmrv02cdf
 cghFLasso               Detecting hot spot on CGH array data with fused
                         lasso regression.
 CGHweb                  analyzing array_CGH data with multiple
                         algorithms
 chron                   Chronological objects which can handle dates
                         and times
 class                   Functions for Classification
 cluster                 Cluster Analysis Extended Rousseeuw et al.
 cnv                     Detection of Copy Number Variation by
                         Sequencing
 CNVtools                A package to test genetic association with CNV
                         data
 coda                    Output analysis and diagnostics for MCMC
 codetools               Code Analysis Tools for R
 colorspace              Color Space Manipulation
 compiler                The R Compiler Package
 corpcor                 Efficient Estimation of Covariance and
                         (Partial) Correlation
 crlmm                   Genotype Calling (CRLMM) and Copy Number
                         Analysis tool for Affymetrix SNP 5.0 and 6.0
                         and Illumina arrays.
 cummeRbund              Analysis, exploration, manipulation, and
                         visualization of Cufflinks high-throughput
                         sequencing data.
 datasets                The R Datasets Package
 DBI                     R Database Interface
 DESeq                   Differential gene expression analysis based on
                         the negative binomial distribution
 deSolve                 General solvers for initial value problems of
                         ordinary differential equations (ODE), partial
                         differential equations (PDE), differential
                         algebraic equations (DAE), and delay
                         differential equations (DDE).
 DEXSeq                  Inference of differential exon usage in RNA-Seq
 dichromat               Color schemes for dichromats
 digest                  Create cryptographic hash digests of R objects
 diversitree             diversitree: comparative phylogenetic analyses
                         of diversification
 DNAcopy                 DNA copy number data analysis
 doMC                    Foreach parallel adaptor for the multicore
                         package
 doParallel              Foreach parallel adaptor for the parallel
                         package
 doSNOW                  Foreach parallel adaptor for the snow package
 dynamicTreeCut          Methods for detection of clusters in
                         hierarchical clustering dendrograms.
 DynDoc                  Dynamic document tools
 e1071                   Misc Functions of the Department of Statistics
                         (e1071), TU Wien
 edgeR                   Empirical analysis of digital gene expression
                         data in R
 effects                 Effect Displays for Linear, Generalized Linear,
                         Multinomial-Logit, Proportional-Odds Logit
                         Models and Mixed-Effects Models
 ellipse                 Functions for drawing ellipses and ellipse-like
                         confidence regions
 EMA                     Easy Microarray data Analysis
 exonmap                 High level analysis of Affymetrix exon array
                         data
 exon.pmcdf              exon.pmcdf
 FactoMineR              Multivariate Exploratory Data Analysis and Data
                         Mining with R
 FASeg                   Forward-backward fragment assembling method for
                         the segmentation of array-based copy number
                         data
 fastcluster             Fast hierarchical clustering routines for R and
                         Python
 fda                     Functional Data Analysis
 fdrtool                 Estimation of (Local) False Discovery Rates and
                         Higher Criticism
 ff                      memory-efficient storage of large data on disk
                         and fast access functions
 flashClust              Implementation of optimal hierarchical
                         clustering
 foreach                 Foreach looping construct for R
 foreign                 Read Data Stored by Minitab, S, SAS, SPSS,
                         Stata, Systat, dBase, ...
 gbm                     Generalized Boosted Regression Models
 gcrma                   Background Adjustment Using Sequence
                         Information
 gdata                   Various R programming tools for data
                         manipulation
 GDD                     GD device for creating bitmap graphics as jpeg,
                         png or gif files using gd library
 gee                     Generalized Estimation Equation solver
 geiger                  Analysis of evolutionary diversification
 GeneCycle               Identification of Periodically Expressed Genes
 genefilter              genefilter: methods for filtering genes from
                         microarray experiments
 GeneNet                 Modeling and Inferring Gene Networks
 geneplotter             Graphics related functions for Bioconductor
 GeneTS                  Microarray Time Series and Network Analysis
 GenomicFeatures         Tools for making and manipulating transcript
                         centric annotations
 GenomicRanges           Representation and manipulation of genomic
                         intervals
 ggplot2                 An implementation of the Grammar of Graphics
 GLAD                    Gain and Loss Analysis of DNA
 glmmADMB                Generalized Linear Mixed Models using AD Model
                         Builder
 GO.db                   A set of annotation maps describing the entire
                         Gene Ontology
 GOstats                 Tools for manipulating GO and microarrays.
 gplots                  Various R programming tools for plotting data
 graph                   graph: A package to handle graph data
                         structures
 graphics                The R Graphics Package
 grDevices               The R Graphics Devices and Support for Colours
                         and Fonts
 grid                    The Grid Graphics Package
 GSA                     Gene set analysis
 GSEABase                Gene set enrichment data structures and methods
 gsubfn                  Utilities for strings and function arguments.
 gtable                  Arrange grobs in tables.
 gtools                  Various R programming tools
 Gviz                    Plotting data and annotation information along
                         genomic coordinates
 heatmap.plus            Heatmap with more sensible behavior.
 hexbin                  Hexagonal Binning Routines
 hgu133plus2.db          Affymetrix Human Genome U133 Plus 2.0 Array
                         annotation data (chip hgu133plus2)
 hgu95av2.db             Affymetrix Human Genome U95 Set annotation data
                         (chip hgu95av2)
 HilbertVis              Hilbert curve visualization
 Hmisc                   Harrell Miscellaneous
 HSAUR2                  A Handbook of Statistical Analyses Using R (2nd
                         Edition)
 hwriter                 HTML Writer - Outputs R objects in HTML format
 impute                  impute: Imputation for microarray data
 IRanges                 Infrastructure for manipulating intervals on
                         sequences
 iterators               Iterator construct for R
 itertools               Iterator Tools
 KEGG.db                 A set of annotation maps for KEGG
 KernSmooth              Functions for kernel smoothing for Wand & Jones
                         (1995)
 labeling                Axis Labeling
 lars                    Least Angle Regression, Lasso and Forward
                         Stagewise
 laser                   Likelihood Analysis of Speciation/Extinction
                         Rates from Phylogenies
 lattice                 Lattice Graphics
 latticeExtra            Extra Graphical Utilities Based on Lattice
 leaps                   regression subset selection
 limma                   Linear Models for Microarray Data
 lme4                    Linear mixed-effects models using S4 classes
 lmtest                  Testing Linear Regression Models
 locfit                  Local Regression, Likelihood and Density
                         Estimation.
 longitudinal            Analysis of Multiple Time Course Data
 lpridge                 Local Polynomial (Ridge) Regression
 maanova                 Tools for analyzing Micro Array experiments
 maDB                    Microarray database and utility functions for
                         microarray data analysis.
 marray                  Exploratory analysis for two-color spotted
                         microarray data
 MASS                    Support Functions and Datasets for Venables and
                         Ripley's MASS
 Matrix                  Sparse and Dense Matrix Classes and Methods
 matrixcalc              Collection of functions for matrix calculations
 matrixStats             Methods that apply to rows and columns of a
                         matrix
 mclust                  Normal Mixture Modeling for Model-Based
                         Clustering, Classification, and Density
                         Estimation
 MCMCpack                Markov chain Monte Carlo (MCMC) Package
 mda                     Mixture and flexible discriminant analysis
 memoise                 Memoise functions
 methods                 Formal Methods and Classes
 mgcv                    Mixed GAM Computation Vehicle with GCV/AIC/REML
                         smoothness estimation
 msm                     Multi-state Markov and hidden Markov models in
                         continuous time
 multcomp                Simultaneous Inference in General Parametric
                         Models
 multicore               Parallel processing of R code on machines with
                         multiple cores or CPUs
 multtest                Resampling-based multiple hypothesis testing
 munsell                 Munsell colour system
 MVA                     An Introduction to Applied Multivariate
                         Analysis with R
 mvtnorm                 Multivariate Normal and t Distributions
 nlme                    Linear and Nonlinear Mixed Effects Models
 nnet                    Feed-forward Neural Networks and Multinomial
                         Log-Linear Models
 oligoClasses            Classes for high-throughput arrays supported by
                         oligo and crlmm
 org.Hs.eg.db            Genome wide annotation for Human
 ouch                    Ornstein-Uhlenbeck models for phylogenetic
                         comparative hypotheses
 parallel                Support for Parallel computation in R
 permute                 Functions for generating restricted
                         permutations of data
 pgUtils                 Utility functions for PostgreSQL databases
 pheatmap                Pretty Heatmaps
 phylobase               Base package for phylogenetic structures and
                         comparative data
 picante                 R tools for integrating phylogenies and ecology
 pixmap                  Bitmap Images (``Pixel Maps'')
 plier                   Implements the Affymetrix PLIER algorithm
 plotrix                 Various plotting functions
 plyr                    Tools for splitting, applying and combining
                         data
 preprocessCore          A collection of pre-processing functions
 prettyR                 Pretty descriptive stats.
 pROC                    display and analyze ROC curves
 proto                   Prototype object-based programming
 PSCBS                   Analysis of Parent-Specific DNA Copy Numbers
 quantreg                Quantile Regression
 qvalue                  Q-value estimation for false discovery rate
                         control
 R2admb                  ADMB to R interface functions
 randomForest            Breiman and Cutler's random forests for
                         classification and regression
 RankProd                Rank Product method for identifying
                         differentially expressed genes with application
                         in meta-analysis
 raster                  raster: Geographic data analysis and modeling
 rasterVis               Visualization methods for the raster package
 RBGL                    An interface to the BOOST graph library
 R.cache                 Fast and light-weight caching (memoization) of
                         objects
 Rcmdr                   R Commander
 RColorBrewer            ColorBrewer palettes
 Rcpp                    Seamless R and C++ Integration
 RcppArmadillo           Rcpp integration for Armadillo templated linear
                         algebra library
 RcppEigen               Rcpp integration for the Eigen templated linear
                         algebra library.
 RCurl                   General network (HTTP/FTP/...) client interface
                         for R
 R.devices               Enhanced methods for handling graphical devices
 relimp                  Relative Contribution of Effects in a
                         Regression Model
 reshape                 Flexibly reshape data.
 reshape2                Flexibly reshape data: a reboot of the reshape
                         package.
 R.filesets              Easy handling of and access to files organized
                         in structured directories
 rgl                     3D visualization device system (OpenGL)
 Rgraphviz               Provides plotting capabilities for R graph
                         objects
 R.huge                  Methods for accessing huge amounts of data
                         [DEPRECATED]
 RMark                   R Code for MARK Analysis
 R.methodsS3             Utility function for defining S3 methods
 RMySQL                  R interface to the MySQL database
 R.oo                    R object-oriented programming with or without
                         references
 rpart                   Recursive Partitioning
 RPostgreSQL             R interface to the PostgreSQL database system
 R.rsp                   Dynamic generation of scientific reports
 Rsamtools               Binary alignment (BAM), variant call (BCF), or
                         tabix file import
 RSQLite                 SQLite interface for R
 RSQLite.extfuns         Math and String Extension Functions for RSQLite
 Rsubread                Rsubread: a super fast, sensitive and accurate
                         read aligner for mapping next-generation
                         sequencing reads
 rtracklayer             R interface to genome browsers and their
                         annotation tracks
 R.utils                 Various programming utilities
 Rwave                   Time-Frequency analysis of 1-D signals
 sandwich                Robust Covariance Matrix Estimators
 scales                  Scale functions for graphics.
 scatterplot3d           3D Scatter Plot
 sem                     Structural Equation Models
 setRNG                  Set (Normal) Random Number Generator and Seed
 siggenes                Multiple testing using SAM and Efron's
                         empirical Bayes approaches
 simpleaffy              Very simple high level analysis of Affymetrix
                         data
 smida                   Statistics for Microarrays: Inference, Design
                         and Analysis
 snapCGH                 Segmentation, normalisation and processing of
                         aCGH data.
 snow                    Simple Network of Workstations
 snowfall                Easier cluster computing (based on snow).
 SNPchip                 Visualizations for copy number alterations
 sp                      classes and methods for spatial data
 SparseM                 Sparse Linear Algebra
 spatial                 Functions for Kriging and Point Pattern
                         Analysis
 splines                 Regression Spline Functions and Classes
 spp                     some description
 sqldf                   Perform SQL Selects on R Data Frames
 statmod                 Statistical Modeling
 stats                   The R Stats Package
 stats4                  Statistical Functions using S4 Classes
 stringr                 Make it easier to work with strings.
 strucchange             Testing, Monitoring, and Dating Structural
                         Changes
 subplex                 Subplex optimization algorithm
 survival                Survival analysis, including penalised
                         likelihood.
 SVGAnnotation           Tools for post-processing SVG plots created in
                         R
 tcltk                   Tcl/Tk Interface
 tilingArray             Transcript mapping with high-density
                         oligonucleotide tiling arrays
 tools                   Tools for Package Development
 truncnorm               Truncated normal distribution
 unmarked                Models for Data from Unmarked Animals
 utils                   The R Utils Package
 vegan                   Community Ecology Package
 vsn                     Variance stabilization and calibration for
                         microarray data
 waveslim                Basic wavelet routines for one-, two- and
                         three-dimensional signal processing
 wavethresh              Wavelets statistics and transforms.
 WGCNA                   Weighted Correlation Network Analysis
 XML                     Tools for parsing and generating XML within R
                         and S-Plus.
 xtable                  Export tables to LaTeX or HTML
 zlibbioc                An R packaged zlib-1.2.5
 zoo                     S3 Infrastructure for Regular and Irregular
                         Time Series (Z's ordered observations)