DESeq2

DOI: 10.18129/B9.bioc.DESeq2    

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: Release (3.6)

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>

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

HTML	R Script	Analyzing RNA-seq data with DESeq2
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, DifferentialExpression, GeneExpression, RNASeq, SAGE, Sequencing, Software, Transcription
Version	1.18.1
In Bioconductor since	BioC 2.12 (R-3.0) (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, IHW, apeglm, ashr, tximport, tximportData, readr, pbapply, airway, pasilla(>= 0.2.10)
SystemRequirements
Enhances
URL	https://github.com/mikelove/DESeq2
Depends On Me	DChIPRep, DEXSeq, FourCSeq, MLSeq, rgsepd, TCC, XBSeq
Imports Me	anamiR, Anaquin, anota2seq, coseq, DaMiRseq, debrowser, DEFormats, DEGreport, DEsubs, DiffBind, eegc, EnrichmentBrowser, FourCSeq, GenoGAM, HTSFilter, ideal, IHWpaper, ImpulseDE2, IntEREst, isomiRs, JunctionSeq, PathoStat, pcaExplorer, regionReport, ReportingTools, SNPhood, systemPipeR, ToPASeq
Suggests Me	apeglm, biobroom, BiocGenerics, BioCor, compcodeR, DASC, derfinder, diffloop, gage, GenomicAlignments, GenomicRanges, Glimma, IHW, JctSeqData, miRmine, oneChannelGUI, OPWeight, phyloseq, progeny, recount, RUVSeq, scran, Single.mTEC.Transcriptomes, subSeq, tximport, variancePartition
Build Report

Package Archives

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

Source Package	DESeq2_1.18.1.tar.gz
Windows Binary	DESeq2_1.18.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	DESeq2_1.18.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DESeq2
Package Short Url	http://bioconductor.org/packages/DESeq2/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive