DESeq

DESeq is an R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression.

The package is available via Bioconductor and can be conveniently installed as follows:

Start an R session and type

source("http://www.bioconductor.org/biocLite.R")
biocLite("DESeq")

The package home page of DESeq is here.

For usage instructions, see the package vignette available from the package home page.

For a description of the statistical method, see our paper:

Simon Anders, Wolfgang Huber: Differential expression analysis for sequence count data
Genome Biology 11 (2010) R106, doi:10.1186/gb-2010-11-10-r106 (open access to full text)

See also the appendix of the vignette for a description of changes to the method since publication of the paper.

Author: Simon Anders; Last change: 2012-06-21.