To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq")

In most cases, you don't need to download the package archive at all.

DESeq

This package is for version 2.10 of Bioconductor; for the stable, up-to-date release version, see 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>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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 Analysing RNA-Seq data with the "DESeq" package
PDF vst.pdf
PDF Reference Manual
Text NEWS

Details

biocViews ChIPseq, DifferentialExpression, HighThroughputSequencing, RNAseq, SAGE, Software
Version 1.8.3
In Bioconductor since BioC 2.6 (R-2.11) (6 years)
License GPL (>= 3)
Depends Biobase(>= 2.13.11), locfit
Imports genefilter, geneplotter, methods, MASS
LinkingTo
Suggests pasilla(>= 0.2.11), vsn
SystemRequirements
Enhances
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
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source DESeq_1.8.3.tar.gz
Windows Binary DESeq_1.8.3.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/DESeq/tree/release-2.10
Package Short Url http://bioconductor.org/packages/DESeq/
Package Downloads Report Download Stats

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