DESeq

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: 2.10

Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution

Author: Simon Anders, EMBL Heidelberg <sanders at fs.tum.de>

Maintainer: Simon Anders <sanders at fs.tum.de>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("DESeq")

Documentation

PDF R Script Analysing RNA-Seq data with the "DESeq" package
PDF R Script vst.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews ChIPseq, DifferentialExpression, HighThroughputSequencing, RNAseq, SAGE, Software
Depends Biobase(>= 2.13.11), locfit
Imports genefilter, geneplotter, methods, MASS
Suggests pasilla(>= 0.2.11), vsn
System Requirements
License GPL (>= 3)
URL http://www-huber.embl.de/users/anders/DESeq
Depends On Me easyRNASeq, pasilla
Imports Me ArrayExpressHTS, DiffBind, EDASeq, rnaSeqMap
Suggests Me DiffBind, EDASeq, GenomicRanges, oneChannelGUI
Version 1.8.3
Since Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source DESeq_1.8.3.tar.gz
Windows Binary DESeq_1.8.3.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary DESeq_1.8.3.tgz
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