What documentation exists for R?

Chapter 5: R Add-On Packages 72
plgem Power Law Global Error Model.
plier Implements the Affymetrix PLIER (Probe Logarithmic Error Intensity Estimate)
algorithm.
prada Tools for analyzing and navigating data from high-throughput phenotyping
experiments based on cellular assays and fluorescent detection.
qtlvalue Q-value estimation for false discovery rate control.
rama Robust Analysis of MicroArrays: robust estimation of cDNA microarray intensities
with replicates using a Bayesian hierarchical model.
reb Regional Expression Biases.
reposTools
Tools for dealing with file repositories and allow users to easily install, update,
and distribute packages, vignettes, and other files.
rfcdmin Data sets for RFlowCyt examples.
rflowcyt Statistical tools and data structures for analytic flow cytometry.
safe Significance Analysis of Function and Expression.
sagenhaft Functions for reading and comparing SAGE (Serial Analysis of Gene Expression)
libraries.
siggenes Identifying differentially expressed genes and estimating the False Discovery
Rate (FDR) with both the Significance Analysis of Microarrays (SAM) and the
Empirical Bayes Analyses of Microarrays (EBAM).
simpleaffy Very simple high level analysis of Affymetrix data.
simulatorAPMS
Computationally simulates the AP-MS technology.
sizepower Sample size and power calculation in microrarray studies.
snapCGH Segmentation, normalization and processing of aCGH data.
splicegear A set of tools to work with alternative splicing.
spotSegmentation
Microarray spot segmentation and gridding for blocks of microarray spots.
sscore S-score algorithm for Affymetrix oligonucleotide microarrays.
ssize Estimate microarry sample size.
stam STructured Analysis of Microarray data.
stepNorm Stepwise normalization functions for cDNA microarrays.
tilingArray
Analysis of tiling arrays.
timecourse
Statistical analysis for developmental microarray time course data.