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