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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 (3.20)

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 <michaelisaiahlove at>

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biocViews Bayesian, ChIPSeq, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, PrincipalComponent, RNASeq, Regression, Sequencing, Software, Transcription
Version 1.45.0
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
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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
Depends On Me DEWSeq, DEXSeq, metaseqR2, octad, rgsepd, rnaseqDTU, rnaseqGene, SeqGSEA, TCC, tRanslatome
Imports Me Anaquin, animalcules, anota2seq, APAlyzer, BatchQC, benchdamic, BloodCancerMultiOmics2017, BRGenomics, CeTF, circRNAprofiler, consensusDE, coseq, countsimQC, cypress, DaMiRseq, debrowser, DEFormats, DEGreport, DELocal, deltaCaptureC, DEsubs, DiffBind, easier, EBSEA, ERSSA, ExpHunterSuite, FieldEffectCrc, GDCRNATools, GeneTonic, gg4way, Glimma, GRaNIE, hermes, homosapienDEE2CellScore, HTSFilter, HybridExpress, icetea, ideal, IHWpaper, INSPEcT, IntEREst, iSEEde, isomiRs, kissDE, magpie, microbiomeExplorer, microbiomeMarker, MIRit, MLSeq, mobileRNA, mosdef, 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, extraChIPs, fishpond, fluentGenomics, gage, GeDi, GenomicAlignments, GenomicRanges, GeoTcgaData, glmGamPoi, GSE62944, HiCDCPlus, IHW, InteractiveComplexHeatmap, methodical, OPWeight, pathlinkR, PCAtools, phyloseq, progeny, PROPER, raer, recount, RegParallel, ribosomeProfilingQC, roastgsa, RUVSeq, Rvisdiff, scran, seqpac, Single.mTEC.Transcriptomes, sparrow, spatialHeatmap, SpliceWiz, subSeq, SummarizedBenchmark, systemPipeR, systemPipeShiny, TFEA.ChIP, tidybulk, topconfects, tximeta, tximport, variancePartition, Wrench, zinbwave
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