DESeq

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: Development (3.0)

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   Reference Manual
Text   NEWS

Details

biocViews ChIPSeq, DifferentialExpression, RNASeq, SAGE, Sequencing, Software
Version 1.17.0
In Bioconductor since BioC 2.6 (R-2.11)
License GPL (>= 3)
Depends BiocGenerics(>= 0.7.5), Biobase(>= 2.21.7), locfit, lattice
Imports genefilter, geneplotter, methods, MASS, RColorBrewer
Suggests pasilla(>= 0.2.10), vsn, gplots
System Requirements
URL http://www-huber.embl.de/users/anders/DESeq
Depends On Me DBChIP, EDDA, metaseqR, parathyroid, SeqGSEA, TCC, tRanslatome
Imports Me ampliQueso, ArrayExpressHTS, easyRNASeq, EDASeq, EDDA, HTSFilter, rnaSeqMap
Suggests Me BitSeq, compcodeR, DESeq2, dexus, DiffBind, EDASeq, ELBOW, gage, gCMAP, genefilter, GenomicAlignments, GenomicRanges, oneChannelGUI, pasilla, SSPA

Package Downloads

Package Source DESeq_1.17.0.tar.gz
Windows Binary DESeq_1.17.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) DESeq_1.17.0.tgz
Mac OS X 10.9 (Mavericks)
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