DESeq2

DOI: 10.18129/B9.bioc.DESeq2  

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: Release (3.16)

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 "4.2") and enter:

if (!require("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 1.38.3
In Bioconductor since BioC 2.12 (R-3.0) (10 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, 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, octad, rgsepd, rnaseqDTU, rnaseqGene, SeqGSEA, TCC, tRanslatome
Imports Me Anaquin, animalcules, anota2seq, APAlyzer, benchdamic, BloodCancerMultiOmics2017, BRGenomics, CeTF, circRNAprofiler, consensusDE, coseq, countsimQC, DaMiRseq, debrowser, DEComplexDisease, DEFormats, DEGreport, deltaCaptureC, DEsubs, DiffBind, easier, EBSEA, eegc, ERSSA, exomePeak2, ExpHunterSuite, FieldEffectCrc, GDCRNATools, GeneTonic, Glimma, GRaNIE, hermes, HTSFilter, icetea, ideal, IHWpaper, INSPEcT, IntEREst, isomiRs, kissDE, microbiomeExplorer, microbiomeMarker, MLSeq, multiSight, muscat, NBAMSeq, NetActivity, ORFik, OUTRIDER, PathoStat, pcaExplorer, phantasus, POMA, proActiv, recountWorkflow, RegEnrich, regionReport, ReportingTools, RiboDiPA, Rmmquant, RNASeqR, scBFA, scGPS, SEtools, singleCellTK, SNPhood, srnadiff, systemPipeTools, TBSignatureProfiler, TEKRABber, TimeSeriesExperiment, UMI4Cats, vidger, vulcan
Suggests Me aggregateBioVar, apeglm, bambu, biobroom, BiocGenerics, BioCor, BiocSet, BioNERO, CAGEr, CAGEWorkflow, compcodeR, curatedAdipoChIP, curatedAdipoRNA, dearseq, derfinder, dittoSeq, EDASeq, EnhancedVolcano, EnrichmentBrowser, EWCE, fishpond, fluentGenomics, gage, GenomicAlignments, GenomicRanges, glmGamPoi, HiCDCPlus, IHW, InteractiveComplexHeatmap, miRmine, NxtIRFcore, OPWeight, PCAtools, phyloseq, progeny, PROPER, recount, RegParallel, RUVSeq, scran, Single.mTEC.Transcriptomes, sparrow, spatialHeatmap, SpliceWiz, subSeq, SummarizedBenchmark, systemPipeR, systemPipeShiny, TFEA.ChIP, tidybulk, 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_1.38.3.tar.gz
Windows Binary DESeq2_1.38.3.zip (64-bit only)
macOS Binary (x86_64) DESeq2_1.38.3.tgz
macOS Binary (arm64) DESeq2_1.38.3.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
Old Source Packages for BioC 3.16 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: