DESeq

Overview

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

DESeq uses a model based on the negative binomial distribution and offers, in brief, the following features:

Download and installation

Automatic installation via Bioconductor

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

The Bioconductor install script (biocLite) ties the package version to the R version used. Hence, if you use the current release version of R, you will get the version of DESeq from the current release version of Bioconductor, and if you use the development version of R, you get the development version of DESeq (i.e., the version containing the newest changes, which may be still unstable.)

However, the DESeq works fine with an older R installation, too. You just need to install it manually, as follows.

Manual installation

Paper and further information

The statistical method behind DESeq is explained in our paper:

Simon Anders and Wolfgang Huber: Differential expression analysis for sequence count data
Genome Biology (2010) 11:R106 (open access)

If you use DESeq in scientific work, please cite this paper in your publication.

The package home page of DESeq is here (release version) and here (development version).

For usage instructions, see the package vignette, for a description of the statistical method, please see our paper.

Author: Simon Anders; Last change: 2010-11-02.

myspace visitor counter