Software

Bioconductor R packages

limma (2002–present) has extensive capabilities for pre-processing and differential expression analysis of microarray experiments.

limmaGUI (2003–present) provides a menu-driven interface to the limma package for analysing two-colour microarray data [41]. Developed by James Wettenhall.

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.

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 the 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.

CRAN R packages

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.

Web tools

ELDA. Extreme limiting dilution analysis for comparing stem cell frequencies between populations.

Compare Growth Curves. Permutation test for comparing groups of growth curves.

S-Plus

I have authored a wide variety statistical modelling functions for S-Plus, although I no longer maintain these.

Matlab

statbox (1990–2001) is a statistics toolbox for Matlab, including ordinal logistic regression and linear mixed models. No longer maintained.