What documentation exists for R?

Chapter 5: R Add-On Packages 66
Biostrings Class definitions and generics for biological sequences along with pattern matching
algorithms.
Category A collection of tools for performing category analysis.
ChromoViz
Draw gene expression profile onto chromosome using SVG.
CoCiteStats
A collection of software tools for dealing with co-citation data.
DEDS Differential Expression via Distance Summary for microarray data.
DNAcopy Segments DNA copy number data using circular binary segmentation to detect
regions with abnormal copy number.
DynDoc Functionality to create and interact with dynamic documents, vignettes, and
other navigable documents.
EBImage R image processing toolkit.
EBarrays Empirical Bayes tools for the analysis of replicated microarray data across multiple
conditions.
GEOquery
Get data from NCBI Gene Expression Omnibus (GEO).
GLAD Gain and Loss Analysis of DNA.
GOstats Tools for manipulating GO and microarrays.
GeneMeta A collection of meta-analysis tools for analyzing high throughput experimental
data.
GeneR Package manipulating nucleotidic sequences (Embl, Fasta, GenBank).
GeneSpring
Functions and class definitions to be able to read and write GeneSpring specific
data objects and convert them to Bioconductor objects.
GeneTS A package for analysing multiple gene expression time series data. Currently,
implements methods for cell cycle analysis and for inferring large sparse graphical
Gaussian models.
GeneTraffic
GeneTraffic R integration functions.
GenomeBase
Base functions for genome data package manipulation.
GlobalAncova
Calculates a global test for differential gene expression between groups.
GraphAT Graph theoretic Association Tests.
HEM Heterogeneous Error Model for analysis of microarray data.
Heatplus A heat map displaying covariates and coloring clusters.