|sw summary=DESeq is an R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression. The latest version is DESeq2 (released April 2013).|bio domain=RNA-Seqquantification, ChIP-seq|bio method=statistical testing, Sequencing quality control,|created by=Anders S|created at=European Molecular Biology Laboratory|maintained=Yes|email address=sanders@fs.tum.de|input format=table with count data|output format=table

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

 Tests for differential expression between two experimental conditions should take into account both technical and biological variability. Recently, several authors have claimed that the Poisson distribution can be used for this purpose. However, tests based on the Poisson assumption (this includes the binomial test and the chi-squared test) ignore the biological sampling variance, leading to incorrectly optimistic p values. The negative binomial distribution is a generalisation of the Poisson model that allows to model biological variance correctly. In the former two points, DESeq is similar to earlier tools, especially to edgeR. One of the new features of DESeq is the ability to estimate the variance in a local fashion, using different coefficients of variation for different expression strengths. This removes potential selection biases in the hit list of differentially expressed genes, and gives a more balanced and accurate result.