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

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DESeq

 

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: Release (3.1)

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>

Citation (from within R, enter citation("DESeq")):

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DESeq")

 

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 1.20.0
In Bioconductor since BioC 2.6 (R-2.11) (5 years)
License GPL (>= 3)
Depends BiocGenerics(>= 0.7.5), Biobase(>= 2.21.7), locfit, lattice
Imports genefilter, geneplotter, methods, MASS, RColorBrewer
LinkingTo
Suggests pasilla(>= 0.2.10), vsn, gplots
SystemRequirements
Enhances
URL http://www-huber.embl.de/users/anders/DESeq
Depends On Me DBChIP, EDDA, metaseqR, Polyfit, SeqGSEA, TCC, tRanslatome
Imports Me ampliQueso, ArrayExpressHTS, easyRNASeq, EDASeq, EDDA, gCMAP, HTSFilter, rnaSeqMap, ToPASeq
Suggests Me BitSeq, compcodeR, DESeq2, dexus, DiffBind, ELBOW, gage, genefilter, GenomicAlignments, GenomicRanges, oneChannelGUI, pasilla, PROPER, RUVSeq, SSPA
Build Report  

Package Archives

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Package Source DESeq_1.20.0.tar.gz
Windows Binary DESeq_1.20.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) DESeq_1.20.0.tgz
Mac OS X 10.9 (Mavericks) DESeq_1.20.0.tgz
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