To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")

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

DESeq2

This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see DESeq2.

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: 3.3

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:// URLs are not supported
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, Transcription
Version	1.12.4
In Bioconductor since	BioC 2.12 (R-3.0) (3.5 years)
License	LGPL (>= 3)
Depends	S4Vectors(>= 0.9.25), IRanges, GenomicRanges, SummarizedExperiment(>= 1.1.6)
Imports	BiocGenerics(>= 0.7.5), Biobase, BiocParallel, genefilter, methods, locfit, geneplotter, ggplot2, Hmisc, Rcpp (>= 0.11.0)
LinkingTo	Rcpp, RcppArmadillo
Suggests	testthat, knitr, BiocStyle, vsn, pheatmap, RColorBrewer, airway, IHW, tximport, tximportData, readr, pasilla(>= 0.2.10), DESeq
SystemRequirements
Enhances
URL
Depends On Me	DChIPRep, DEXSeq, FourCSeq, MLSeq, rgsepd, TCC, XBSeq
Imports Me	debrowser, DEFormats, DiffBind, EnrichmentBrowser, FourCSeq, GenoGAM, Glimma, HTSFilter, IHWpaper, isomiRs, JunctionSeq, pcaExplorer, regionReport, ReportingTools, SNPhood, systemPipeR, ToPASeq
Suggests Me	biobroom, BiocGenerics, compcodeR, derfinder, gage, GenomicAlignments, GenomicRanges, IHW, IHW, JctSeqData, oneChannelGUI, phyloseq, RUVSeq, scran, Single.mTEC.Transcriptomes, subSeq, tximport, variancePartition
Build Report

Package Archives

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

Package Source	DESeq2_1.12.4.tar.gz
Windows Binary	DESeq2_1.12.4.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks)	DESeq2_1.12.4.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/DESeq2/tree/release-3.3
Package Short Url	http://bioconductor.org/packages/DESeq2/
Package Downloads Report	Download Stats

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