DESeq2 (original) (raw)

This is the released version of DESeq2; for the devel version, seeDESeq2.

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: Release (3.20)

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

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")

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")

Details

biocViews Bayesian, ChIPSeq, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, PrincipalComponent, RNASeq, Regression, Sequencing, Software, Transcription
Version 1.46.0
In Bioconductor since BioC 2.12 (R-3.0) (11.5 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, SeqGSEA, TCC, tRanslatome, rnaseqDTU, rnaseqGene, Anaconda, DRomics, ordinalbayes
Imports Me Anaquin, animalcules, APAlyzer, BatchQC, broadSeq, CeTF, circRNAprofiler, CleanUpRNAseq, consensusDE, coseq, countsimQC, cypress, DaMiRseq, debrowser, DEFormats, DEGreport, DELocal, deltaCaptureC, DEsubs, DiffBind, easier, EBSEA, ERSSA, GDCRNATools, GeneTonic, gg4way, Glimma, GRaNIE, hermes, HTSFilter, HybridExpress, icetea, ideal, INSPEcT, IntEREst, iSEEde, isomiRs, kissDE, magpie, MIRit, MLSeq, mobileRNA, mosdef, MultiRNAflow, muscat, NBAMSeq, NetActivity, ORFik, OUTRIDER, pairedGSEA, PathoStat, pcaExplorer, phantasus, POMA, proActiv, RegEnrich, regionReport, ReportingTools, RiboDiPA, Rmmquant, saseR, scBFA, scGPS, SEtools, singleCellTK, SNPhood, systemPipeTools, TEKRABber, UMI4Cats, vidger, vulcan, zitools, BloodCancerMultiOmics2017, FieldEffectCrc, homosapienDEE2CellScore, IHWpaper, ExpHunterSuite, recountWorkflow, bulkAnalyseR, cinaR, ExpGenetic, ggpicrust2, HeritSeq, limorhyde2, MetaLonDA, microbial, RCPA, RNAseqQC, sRNAGenetic, wilson
Suggests Me aggregateBioVar, apeglm, bambu, BindingSiteFinder, biobroom, BiocGenerics, BioCor, BiocSet, BioNERO, CAGEr, compcodeR, dar, dearseq, derfinder, dittoSeq, EDASeq, EnhancedVolcano, EnrichmentBrowser, EWCE, extraChIPs, fishpond, gage, GeDi, GenomicAlignments, GenomicRanges, GeoTcgaData, glmGamPoi, HiCDCPlus, IHW, InteractiveComplexHeatmap, OPWeight, pathlinkR, PCAtools, phyloseq, progeny, raer, recount, ribosomeProfilingQC, roastgsa, RUVSeq, Rvisdiff, scran, sparrow, spatialHeatmap, SpliceWiz, subSeq, systemPipeR, systemPipeShiny, TFEA.ChIP, tidybulk, topconfects, tximeta, tximport, variancePartition, Wrench, zinbwave, curatedAdipoChIP, curatedAdipoRNA, GSE62944, RegParallel, Single.mTEC.Transcriptomes, CAGEWorkflow, fluentGenomics, seqpac, bakR, cellpypes, conos, FateID, GiANT, glmmSeq, grandR, lfc, LorMe, metaRNASeq, MiscMetabar, pctax, pmartR, RaceID, rliger, SCdeconR, seqgendiff, Seurat, SQMtools, volcano3D
Links To Me
Build Report Build Report

Package Archives

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

Source Package DESeq2_1.46.0.tar.gz
Windows Binary (x86_64) DESeq2_1.46.0.zip (64-bit only)
macOS Binary (x86_64) DESeq2_1.46.0.tgz
macOS Binary (arm64) DESeq2_1.46.0.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