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