DESeq2
Differential gene expression analysis based on the negative binomial distribution
Bioconductor version: 3.23 · Package version: 1.52.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2")Details
| Maintainer | Michael Love <michaelisaiahlove@gmail.com> |
| Author | Michael Love [aut, cre], Constantin Ahlmann-Eltze [ctb], Anqi Zhu [ctb], Nikolaos Ignatiadis [ctb], Raphael Rossellini [ctb], Kwame Forbes [ctb], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb], RADIANT EU FP7 [fnd], NIH NHGRI [fnd], CZI [fnd] |
| License | LGPL (>= 3) |
| URL | https://github.com/thelovelab/DESeq2 |
| Downloads rank | 30566 |
| Source branch | RELEASE_3_23 |
| biocViews | Bayesian, ChIPSeq, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, PrincipalComponent, RNASeq, Regression, Sequencing, Software, Transcription |
Documentation
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Dependencies
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
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, glmGamPoi, BiocManager
Reverse dependencies
Depends On Me (13): Anaconda, DEWSeq, DEXSeq, DRomics, metaseqR2, octad, ordinalbayes, rgsepd, rnaseqDTU, rnaseqGene, SeqGSEA, TCC, tRanslatome
Imports Me (104): Anaquin, animalcules, anota2seq, APAlyzer, autoGO, BatchQC, benchdamic, BloodCancerMultiOmics2017, broadSeq, carnation, CeTF, cinaR, circRNAprofiler, CleanUpRNAseq, coseq, countsimQC, cypress, DaMiRseq, debrowser, DeeDeeExperiment, DEFormats, DEGreport, DELocal, deltaCaptureC, DEsubs, DiffBind, DOtools, DOTSeq, DspikeIn, easier, EBSEA, ERSSA, ExpGenetic, ExpHunterSuite, FieldEffectCrc, fourSynergy, GDCRNATools, GeneTonic, gg4way, Glimma, GRaNIE, hermes, HEssRNA, HTSFilter, HybridExpress, icetea, ideal, IHWpaper, INSPEcT, IntEREst, iSEEde, isomiRs, kissDE, limorhyde2, magpie, microbial, microbiomeExplorer, MIRit, MLSeq, mobileRNA, mosdef, MultiRNAflow, NBAMSeq, NetActivity, ORFik, OUTRIDER, pairedGSEA, PathoStat, pcaExplorer, phantasus, POMA, power.nb, proActiv, RCPA, recountWorkflow, RegEnrich, regionReport, ReportingTools, RiboDiPA, Rmmquant, RNAseqQC, saseR, scBFA, scECODA, scGPS, scQTLtools, SEtools, singleCellTK, SNPhood, srnadiff, sRNAGenetic, SurfR, systemPipeTools, TBSignatureProfiler, TEKRABber, terapadog, TransProR, UMI4Cats, vidger, VISTA, vulcan, wilson, XYomics, zitools
Suggests Me (97): aggregateBioVar, apeglm, bakR, bambu, BindingSiteFinder, biobroom, BiocGenerics, BioCor, BiocSet, BioNERO, CAGEr, CAGEWorkflow, ChIPDBData, compcodeR, conos, curatedAdipoChIP, curatedAdipoRNA, dar, dearseq, dependentsimr, derfinder, dittoSeq, EDASeq, EnhancedVolcano, EnrichmentBrowser, EWCE, extraChIPs, FateID, fishpond, fluentGenomics, futurize, gage, GeDi, genefindr, GenomicAlignments, GenomicRanges, GeoTcgaData, geyser, ggpicrust2, GiANT, glmGamPoi, glmmSeq, grandR, GSE62944, HiCDCPlus, IHW, InteractiveComplexHeatmap, IOBR, lfc, LorMe, metacoder, metaRNASeq, MiscMetabar, muscat, myTAI, OPWeight, pathlinkR, PCAtools, pctax, phyloseq, pmartR, progeny, PROPER, QRscore, RaceID, raer, recount, RegParallel, RFGeneRank, ribosomeProfilingQC, rliger, roastgsa, RUVSeq, Rvisdiff, scran, scToppR, seqgendiff, seqpac, Seurat, SeuratExplorer, Single.mTEC.Transcriptomes, sparrow, spatialHeatmap, SpliceWiz, subSeq, systemPipeR, systemPipeShiny, TFEA.ChIP, tidybulk, topconfects, tximeta, tximport, variancePartition, venny, volcano3D, Wrench, zinbwave