DESeq2

DOI: 10.18129/B9.bioc.DESeq2    

This is the development version of DESeq2; for the stable release version, see DESeq2.

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: Development (3.8)

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:

if (!require("BiocManager"))
    install.packages("BiocManager")
BiocManager::install("DESeq2", version = "devel")

Documentation

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

browseVignettes("DESeq2")

 

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

Details

biocViews Bayesian, ChIPSeq, Clustering, DifferentialExpression, GeneExpression, Microbiome, Normalization, PrincipalComponent, RNASeq, Regression, Sequencing, Software, Transcription
Version 1.21.10
In Bioconductor since BioC 2.12 (R-3.0) (5.5 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, rmarkdown, 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, rgsepd, rnaseqGene, TCC, XBSeq
Imports Me anamiR, Anaquin, anota2seq, BloodCancerMultiOmics2017, coseq, DaMiRseq, debrowser, DEComplexDisease, DEFormats, DEGreport, DEsubs, DiffBind, eegc, EnrichmentBrowser, FourCSeq, GDCRNATools, GenoGAM, HTSFilter, ideal, IHWpaper, ImpulseDE2, IntEREst, isomiRs, JunctionSeq, kissDE, MLSeq, OUTRIDER, PathoStat, pcaExplorer, PowerExplorer, recountWorkflow, regionReport, ReportingTools, Rmmquant, singleCellTK, SNPhood, srnadiff, systemPipeR, vidger
Suggests Me apeglm, biobroom, BiocGenerics, BioCor, compcodeR, derfinder, diffloop, gage, GenomicAlignments, GenomicRanges, Glimma, gsean, IHW, JctSeqData, miRmine, OPWeight, phyloseq, progeny, recount, RUVSeq, scran, Single.mTEC.Transcriptomes, subSeq, SummarizedBenchmark, TFEA.ChIP, tximport, variancePartition, zinbwave
Build Report  

Package Archives

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

Source Package DESeq2_1.21.10.tar.gz
Windows Binary DESeq2_1.21.10.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) DESeq2_1.21.10.tgz
Source Repository git clone https://git.bioconductor.org/packages/DESeq2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DESeq2
Package Short Url http://bioconductor.org/packages/DESeq2/
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