R libraries

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
akima                   Interpolation of irregularly spaced data
annaffy                 Annotation tools for Affymetrix biological
                        metadata
annotate                Annotation for microarrays
AnnotationDbi           Annotation Database Interface
ape                     Analyses of Phylogenetics and Evolution
base                    The R Base Package
baySeq                  Empirical Bayesian analysis of patterns of
                        differential expression in count data
Biobase                 Biobase: Base functions for Bioconductor
BiocGenerics            Generic functions for Bioconductor
BiocInstaller           Install/Update Bioconductor and CRAN Packages
Biostrings              String objects representing biological
                        sequences, and matching algorithms
bitops                  Functions for Bitwise operations
boot                    Bootstrap Functions (originally by Angelo Canty
                        for S)
caTools                 Tools: moving window statistics, GIF, Base64,
                        ROC AUC, etc.
class                   Functions for Classification
cluster                 Cluster Analysis Extended Rousseeuw et al.
CNVtools                A package to test genetic association with CNV
                        data
codetools               Code Analysis Tools for R
colorspace              Color Space Manipulation
compiler                The R Compiler Package
datasets                The R Datasets Package
DBI                     R Database Interface
DESeq                   Differential gene expression analysis based on
                        the negative binomial distribution
dichromat               Color schemes for dichromats
digest                  Create cryptographic hash digests of R objects
doMC                    Foreach parallel adaptor for the multicore
                        package
doSNOW                  Foreach parallel adaptor for the snow package
DynDoc                  Dynamic document tools
edgeR                   Empirical analysis of digital gene expression
                        data in R
foreach                 Foreach looping construct for R
foreign                 Read Data Stored by Minitab, S, SAS, SPSS,
                        Stata, Systat, dBase, ...
gcrma                   Background Adjustment Using Sequence
                        Information
gdata                   Various R programming tools for data
                        manipulation
gee                     Generalized Estimation Equation solver
geiger                  Analysis of evolutionary diversification
genefilter              genefilter: methods for filtering genes from
                        microarray experiments
geneplotter             Graphics related functions for Bioconductor
GenomicRanges           Representation and manipulation of genomic
                        intervals
ggplot2                 An implementation of the Grammar of Graphics