What documentation exists for R?

Chapter 5: R Add-On Packages 71
logicFS Identification of SNP interactions.
maCorrPlot
Visualize artificial correlation in microarray data.
maDB Microarray database and utility functions for microarray analysis.
maSigPro Significant gene expression profile differeneces in time course microarray data.
maanova Tools for analyzing micro array experiments.
macat MicroArray Chromosome Analysis Tool.
made4 Multivariate analysis of microarray data using ADE4.
makecdfenv
Two functions. One reads a Affymetrix chip description file (CDF) and creates a
hash table environment containing the location/probe set membership mapping.
The other creates a package that automatically loads that environment.
marray Exploratory analysis for two-color spotted microarray data.
matchprobes
Tools for sequence matching of probes on arrays.
metaArray
Integration of microarray data for meta-analysis.
mmgmos Multi-chip Modified Gamma Model of Oligonucleotide Signal.
multtest Multiple testing procedures for controlling the family-wise error rate (FWER)
and the false discovery rate (FDR). Tests can be based on t- or F -statistics
for one- and two-factor designs, and permutation procedures are available to
estimate adjusted p-values.
nnNorm Spatial and intensity based normalization of cDNA microarray data based on
robust neural nets.
nudge Normal Uniform Differential Gene Expression detection.
ontoTools Graphs and sparse matrices for working with ontologies; formal objects for
nomenclatures with provenance management.
pairseqsim
Pairwise sequence alignment and scoring algorithms for global, local and overlap
alignment with affine gap penalty.
pamr Pam: Prediction Analysis for Microarrays.
panp Presence-Absence calls from Negative strand matching Probesets.
pathRender
Render molecular pathways.
pdmclass CLASSification of microarray samples using Penalized Discriminant Methods.
pgUtils Utility functions for PostgreSQL databases.
pickgene Adaptive gene picking for microarray expression data analysis.