What documentation exists for R?

Chapter 5: R Add-On Packages 70
factDesign A set of tools for analyzing data from factorial designed microarray experiments.
The functions can be used to evaluate appropriate tests of contrast and perform
single outlier detection.
fdrame FDR Adjustments of Microarray Experiments (FDR-AME).
gcrma Background adjustment using sequence information.
genArise A tool for dual color microarray data.
geneRecommender
A gene recommender algorithm to identify genes coexpressed with a query set
of genes.
genefilter Tools for sequentially filtering genes using a wide variety of filtering functions.
Example of filters include: number of missing value, coefficient of variation of
expression measures, ANOVA p-value, Cox model p-values. Sequential application
of filtering functions to genes.
geneplotter
gff3Plotter
Graphical tools for genomic data, for example for plotting expression data along
a chromosome or producing color images of expression data matrices.
Plotting data of experiments on the genomic layout.
globaltest Testing globally whether a group of genes is significantly related to some clinical
variable of interest.
goCluster Analysis of clustering results in conjunction with annotation data.
goTools Functions for description/comparison of oligo ID list using the Gene Ontology
database.
gpls Classification using generalized partial least squares for two-group and multigroup
classification.
graph Classes and tools for creating and manipulating graphs within R.
gtkWidgets
Widgets built using RGtk.
hexbin Binning functions, in particular hexagonal bins for graphing.
hopach Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH).
hypergraph
Capabilities for representing and manipulating hypergraphs.
iSPlot Link views that are based on the same data set.
idiogram Plotting genomic data by chromosomal location.
impute Imputation for microarray data (currently KNN only).
limma Linear models for microarray data.
limmaGUI
Graphical User Interface for package limma.