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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 (3.19)

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>

Citation (from within R, enter citation("DESeq2")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Bayesian, ChIPSeq, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, PrincipalComponent, RNASeq, Regression, Sequencing, Software, Transcription
Version 1.43.4
In Bioconductor since BioC 2.12 (R-3.0) (11 years)
License LGPL (>= 3)
Depends S4Vectors(>= 0.23.18), IRanges, GenomicRanges, SummarizedExperiment(>= 1.1.6)
Imports BiocGenerics(>= 0.7.5), Biobase, BiocParallel, matrixStats, methods, stats4, locfit, ggplot2 (>= 3.4.0), Rcpp (>= 0.11.0), MatrixGenerics
System Requirements
URL https://github.com/thelovelab/DESeq2
See More
Suggests testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, pasilla(>= 0.2.10), glmGamPoi, BiocManager
Linking To Rcpp, RcppArmadillo
Enhances
Depends On Me DEWSeq, DEXSeq, metaseqR2, octad, rgsepd, rnaseqDTU, rnaseqGene, SeqGSEA, TCC, tRanslatome
Imports Me Anaquin, animalcules, anota2seq, APAlyzer, benchdamic, BloodCancerMultiOmics2017, BRGenomics, CeTF, circRNAprofiler, consensusDE, coseq, countsimQC, DaMiRseq, debrowser, DEFormats, DEGreport, DELocal, deltaCaptureC, DEsubs, DiffBind, easier, EBSEA, eegc, ERSSA, exomePeak2, ExpHunterSuite, FieldEffectCrc, GDCRNATools, GeneTonic, gg4way, Glimma, GRaNIE, hermes, HTSFilter, icetea, ideal, IHWpaper, INSPEcT, IntEREst, iSEEde, isomiRs, kissDE, magpie, microbiomeExplorer, microbiomeMarker, MIRit, MLSeq, mobileRNA, MultiRNAflow, muscat, NBAMSeq, NetActivity, ORFik, OUTRIDER, pairedGSEA, PathoStat, pcaExplorer, phantasus, POMA, proActiv, recountWorkflow, RegEnrich, regionReport, ReportingTools, RiboDiPA, Rmmquant, saseR, scBFA, scGPS, SEtools, singleCellTK, SNPhood, srnadiff, SurfR, systemPipeTools, TBSignatureProfiler, TEKRABber, UMI4Cats, vidger, vulcan
Suggests Me aggregateBioVar, apeglm, bambu, BindingSiteFinder, biobroom, BiocGenerics, BioCor, BiocSet, BioNERO, CAGEr, CAGEWorkflow, CBNplot, compcodeR, curatedAdipoChIP, curatedAdipoRNA, dar, dearseq, derfinder, dittoSeq, EDASeq, EnhancedVolcano, EnrichmentBrowser, EWCE, fishpond, fluentGenomics, gage, GenomicAlignments, GenomicRanges, GeoTcgaData, glmGamPoi, GSE62944, HiCDCPlus, IHW, InteractiveComplexHeatmap, methodical, miRmine, OPWeight, pathlinkR, PCAtools, phyloseq, progeny, PROPER, raer, recount, RegParallel, roastgsa, RUVSeq, Rvisdiff, scran, seqpac, Single.mTEC.Transcriptomes, sparrow, spatialHeatmap, SpliceWiz, subSeq, SummarizedBenchmark, systemPipeR, systemPipeShiny, TFEA.ChIP, tidybulk, topconfects, tximeta, tximport, variancePartition, Wrench, zinbwave
Links To Me
Build Report Build Report

Package Archives

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

Source Package DESeq2_1.43.4.tar.gz
Windows Binary DESeq2_1.43.4.zip
macOS Binary (x86_64) DESeq2_1.43.4.tgz
macOS Binary (arm64) DESeq2_1.43.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/DESeq2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DESeq2
Bioc Package Browser https://code.bioconductor.org/browse/DESeq2/
Package Short Url https://bioconductor.org/packages/DESeq2/
Package Downloads Report Download Stats