What documentation exists for R?

Chapter 5: R Add-On Packages 69
annotate Associate experimental data in real time to biological metadata from web databases
such as GenBank, LocusLink and PubMed. Process and store query
results. Generate HTML reports of analyses.
apComplex
Estimate protein complex membership using AP-MS protein data.
applera Tools for Applied Biosystems microarrays AB1700 data analysis and quality
controls.
arrayMagic
Utilities for quality control and processing for two-color cDNA microarray data.
arrayQuality
Performing print-run and array level quality assessment.
beadarray Quality control and low-level analysis of BeadArrays.
bim Bayesian interval mapping diagnostics: functions to interpret QTLCart and
Bmapqtl samples.
bioDist A collection of software tools for calculating distance measures.
biocViews Categorized views of R package repositories.
biomaRt Interface to BioMart databases (e.g., Ensembl)
bridge Bayesian Robust Inference for Differential Gene Expression.
cellHTS Analysis of cell-based screens.
cghMCR Find chromosome regions showing common gains/losses.
clusterStab
Compute cluster stability scores for microarray data.
codelink Manipulation of Codelink Bioarrays data.
convert Convert Microarray Data Objects.
copa Functions to perform cancer outlier profile analysis.
ctc Tools to export and import Tree and Cluster to other programs.
daMA Functions for the efficient design of factorial two-color microarray experiments
and for the statistical analysis of factorial microarray data.
diffGeneAnalysis
Performs differential Gene expression Analysis.
ecolitk Metadata and tools to work with E. coli.
edd Expression density diagnostics: graphical methods and pattern recognition algorithms
for distribution shape classification.
exprExternal
Implementation of exprSet using externalVectors.
externalVector
Basic class definitions and generics for external pointer based vector objects for
R.