To install this package, start R and enter:

## try http if https is not available
source("https://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 (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: 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:

## try http if https is not available
source("https://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   Reference Manual
Text   NEWS

Details

biocViews ChIPSeq, DifferentialExpression, GeneExpression, RNASeq, SAGE, Sequencing, Software
Version 1.8.1
In Bioconductor since BioC 2.12 (R-3.0) (2.5 years)
License LGPL (>= 3)
Depends S4Vectors, IRanges, GenomicRanges, Rcpp (>= 0.10.1), RcppArmadillo (>= 0.3.4.4)
Imports BiocGenerics(>= 0.7.5), Biobase, BiocParallel, genefilter, methods, locfit, geneplotter, ggplot2, Hmisc
LinkingTo Rcpp, RcppArmadillo
Suggests testthat, gplots, knitr, RColorBrewer, BiocStyle, airway, pasilla(>= 0.2.10), DESeq, vsn
SystemRequirements
Enhances
URL
Depends On Me DEXSeq, FourCSeq, MLSeq, rgsepd, TCC
Imports Me EnrichmentBrowser, FourCSeq, HTSFilter, phyloseq, ReportingTools, systemPipeR, ToPASeq
Suggests Me BiocGenerics, compcodeR, DiffBind, gage, oneChannelGUI
Build Report  

Package Archives

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

Package Source DESeq2_1.8.1.tar.gz
Windows Binary DESeq2_1.8.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) DESeq2_1.8.1.tgz
Mac OS X 10.9 (Mavericks) DESeq2_1.8.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/DESeq2/tree/release-3.1
Package Short Url http://bioconductor.org/packages/DESeq2/
Package Downloads Report Download Stats

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