To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("DESeq2")

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

DESeq2

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: Release (2.14)

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: Michael Love (HSPH Boston), Simon Anders, Wolfgang Huber (EMBL Heidelberg)

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

Citation (from within R, enter citation("DESeq2")):

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("DESeq2")

Documentation

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

browseVignettes("DESeq2")

 

PDF R Script Analyzing RNA-Seq data with the "DESeq2" package
PDF R Script Beginner's guide to the "DESeq2" package
PDF   Reference Manual
Text   NEWS

Details

biocViews ChIPSeq, DifferentialExpression, RNASeq, SAGE, Sequencing, Software
Version 1.4.5
In Bioconductor since BioC 2.12 (R-3.0)
License GPL (>= 3)
Depends GenomicRanges, IRanges, Rcpp (>= 0.10.1), RcppArmadillo (>= 0.3.4.4)
Imports BiocGenerics(>= 0.7.5), methods, locfit, genefilter, geneplotter, RColorBrewer, lattice
Suggests RUnit, gplots, knitr, Biobase, BiocStyle, parathyroidSE, pasilla(>= 0.2.10), DESeq, vsn, GenomicAlignments, GenomicFeatures, Rsamtools, biomaRt
System Requirements
URL
Depends On Me DEXSeq, MLSeq, TCC
Imports Me HTSFilter, phyloseq, ReportingTools
Suggests Me BiocGenerics, compcodeR, DiffBind, gage

Package Archives

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

Package Source DESeq2_1.4.5.tar.gz
Windows Binary DESeq2_1.4.5.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) DESeq2_1.4.5.tgz
Mac OS X 10.9 (Mavericks) DESeq2_1.4.5.tgz
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