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 3.4 of Bioconductor; for the stable, up-to-date release version, see DESeq2.

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: 3.4

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, Simon Anders, Wolfgang Huber

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 1.14.1
In Bioconductor since BioC 2.12 (R-3.0) (4 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)
SystemRequirements
Enhances
URL
Depends On Me ASpli, DChIPRep, DEXSeq, FourCSeq, MLSeq, rgsepd, TCC, XBSeq
Imports Me anamiR, debrowser, DEFormats, DEsubs, DiffBind, eegc, EnrichmentBrowser, FourCSeq, GenoGAM, Glimma, HTSFilter, IHWpaper, isomiRs, JunctionSeq, pcaExplorer, regionReport, ReportingTools, SNPhood, systemPipeR, ToPASeq
Suggests Me biobroom, BiocGenerics, compcodeR, DEGreport, derfinder, diffloop, gage, GenomicAlignments, GenomicRanges, IHW, JctSeqData, oneChannelGUI, phyloseq, recount, 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_1.14.1.tar.gz
Windows Binary DESeq2_1.14.1.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) DESeq2_1.14.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/DESeq2/tree/release-3.4
Package Short Url http://bioconductor.org/packages/DESeq2/
Package Downloads Report Download Stats

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