DESeq2

DOI: 10.18129/B9.bioc.DESeq2    

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: Release (3.13)

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 [aut, cre], Constantin Ahlmann-Eltze [ctb], Kwame Forbes [ctb], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb], RADIANT EU FP7 [fnd], NIH NHGRI [fnd], CZI [fnd]

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DESeq2")

For older versions of R, please refer to the appropriate Bioconductor release.

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, ImmunoOncology, Normalization, PrincipalComponent, RNASeq, Regression, Sequencing, Software, Transcription
Version	1.32.0
In Bioconductor since	BioC 2.12 (R-3.0) (8.5 years)
License	LGPL (>= 3)
Depends	S4Vectors(>= 0.23.18), IRanges, GenomicRanges, SummarizedExperiment(>= 1.1.6)
Imports	BiocGenerics(>= 0.7.5), Biobase, BiocParallel, genefilter, methods, stats4, locfit, geneplotter, ggplot2, Rcpp (>= 0.11.0)
LinkingTo	Rcpp, RcppArmadillo
Suggests	testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, pasilla(>= 0.2.10), glmGamPoi, BiocManager
SystemRequirements
Enhances
URL	https://github.com/mikelove/DESeq2
Depends On Me	DEWSeq, DEXSeq, metaseqR2, rgsepd, rnaseqDTU, rnaseqGene, SeqGSEA, TCC, tRanslatome, XBSeq
Imports Me	Anaquin, animalcules, anota2seq, APAlyzer, BioNERO, BloodCancerMultiOmics2017, BRGenomics, CeTF, circRNAprofiler, consensusDE, coseq, countsimQC, crossmeta, DaMiRseq, debrowser, DEComplexDisease, DEFormats, DEGreport, deltaCaptureC, DEsubs, DiffBind, EBSEA, eegc, ERSSA, exomePeak2, ExpHunterSuite, FieldEffectCrc, GDCRNATools, GeneTonic, GenoGAM, Glimma, HTSFilter, icetea, ideal, IHWpaper, INSPEcT, IntEREst, isomiRs, kissDE, microbiomeExplorer, MLSeq, multiSight, muscat, NBAMSeq, ORFik, OUTRIDER, PathoStat, pcaExplorer, phantasus, proActiv, recountWorkflow, RegEnrich, regionReport, ReportingTools, RiboDiPA, Rmmquant, RNASeqR, scBFA, scGPS, SEtools, singleCellTK, SNPhood, spatialHeatmap, srnadiff, systemPipeR, systemPipeTools, TBSignatureProfiler, TimeSeriesExperiment, UMI4Cats, vidger, vulcan
Suggests Me	aggregateBioVar, apeglm, bambu, biobroom, BiocGenerics, BioCor, BiocSet, CAGEr, CAGEWorkflow, compcodeR, curatedAdipoChIP, curatedAdipoRNA, dearseq, derfinder, diffloop, dittoSeq, EDASeq, EnhancedVolcano, EnrichmentBrowser, fishpond, fluentGenomics, gage, GenomicAlignments, GenomicRanges, glmGamPoi, HiCDCPlus, IHW, InteractiveComplexHeatmap, JctSeqData, miRmine, OPWeight, PCAtools, phyloseq, progeny, PROPER, recount, RegParallel, RUVSeq, scran, Single.mTEC.Transcriptomes, subSeq, SummarizedBenchmark, systemPipeShiny, TFEA.ChIP, tidybulk, ToPASeq, topconfects, tximeta, tximport, variancePartition, Wrench, zinbwave
Links To Me
Build Report

Package Archives

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

Source Package	DESeq2_1.32.0.tar.gz
Windows Binary	DESeq2_1.32.0.zip
macOS 10.13 (High Sierra)	DESeq2_1.32.0.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	https://bioconductor.org/packages/DESeq2/
Package Downloads Report	Download Stats