limma (2002–present) has extensive capabilities for pre-processing and differential expression analysis of microarray and RNA-seq experiments.
limmaGUI (2003–present) provides a menu-driven interface to the limma package for analysing two-colour microarray data [41]. Developed by James Wettenhall and maintained by me.
affylmGUI (2004–present) provides a menu-driven interface to the affy, gcrma, affyPLM and limma packages for analysing Affymetrix microarray data [49]. Developed by James Wettenhall and maintained by me.
edgeR (2008–present) performs differential analysis of RNA-Seq, ChIP-Seq and deepSAGE experiments. Is able to separate technical from biological variation and to borrow strength between transcripts or tags.
goseq (2009–present) provides functional analysis of gene lists from RNA-Seq experiments, adjusting for gene length bias. Authored by Matt Young and maintained by Nadia Davidson.
csaw (2014–present) performs differential binding analyses of ChIP-seq experiments. Developed and maintained by Aaron Lun. See the Bioconductor Newsletter article on An overview of the csaw package.
diffHic (2015–present) performs differential interaction analyses of Hi-C experiments. Developed and maintained by Aaron Lun.
statmod (2001–present). An R package for biostatistical modelling, including REML analyses, Tweedie generalized linear models, comparative growth curve analysis, and limiting dilution analyses.
dglm. Double generalized linear models.
tweedie. Functions for Tweedie distributions, exponential family distributions with power-variance functions. Maintained by Peter Dunn.
ELDA. Extreme limiting dilution analysis for comparing stem cell frequencies between populations.
Compare Growth Curves. Permutation test for comparing groups of growth curves.
statbox (1990–2001) is a statistics toolbox for Matlab, including ordinal logistic regression and linear mixed models. No longer maintained.