DESeq2
DOI:
10.18129/B9.bioc.DESeq2
Differential gene expression analysis based on the negative binomial distribution
Bioconductor version: Release (3.13)
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
"4.1") and enter:
if (!requireNamespace("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 |
1.32.0 |
In Bioconductor since |
BioC 2.12 (R-3.0) (8.5 years) |
License |
LGPL (>= 3) |
Depends |
S4Vectors(>= 0.23.18), IRanges, GenomicRanges, SummarizedExperiment(>= 1.1.6) |
Imports |
BiocGenerics(>= 0.7.5), Biobase, BiocParallel, genefilter, 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 |
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Enhances |
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URL |
https://github.com/mikelove/DESeq2 |
Depends On Me |
DEWSeq, DEXSeq, metaseqR2, rgsepd, rnaseqDTU, rnaseqGene, SeqGSEA, TCC, tRanslatome, XBSeq |
Imports Me |
Anaquin, animalcules, anota2seq, APAlyzer, BioNERO, BloodCancerMultiOmics2017, BRGenomics, CeTF, circRNAprofiler, consensusDE, coseq, countsimQC, crossmeta, DaMiRseq, debrowser, DEComplexDisease, DEFormats, DEGreport, deltaCaptureC, DEsubs, DiffBind, EBSEA, eegc, ERSSA, exomePeak2, ExpHunterSuite, FieldEffectCrc, GDCRNATools, GeneTonic, GenoGAM, Glimma, HTSFilter, icetea, ideal, IHWpaper, INSPEcT, IntEREst, isomiRs, kissDE, microbiomeExplorer, MLSeq, multiSight, muscat, NBAMSeq, ORFik, OUTRIDER, PathoStat, pcaExplorer, phantasus, proActiv, recountWorkflow, RegEnrich, regionReport, ReportingTools, RiboDiPA, Rmmquant, RNASeqR, scBFA, scGPS, SEtools, singleCellTK, SNPhood, spatialHeatmap, srnadiff, systemPipeR, systemPipeTools, TBSignatureProfiler, TimeSeriesExperiment, UMI4Cats, vidger, vulcan |
Suggests Me |
aggregateBioVar, apeglm, bambu, biobroom, BiocGenerics, BioCor, BiocSet, CAGEr, CAGEWorkflow, compcodeR, curatedAdipoChIP, curatedAdipoRNA, dearseq, derfinder, diffloop, dittoSeq, EDASeq, EnhancedVolcano, EnrichmentBrowser, fishpond, fluentGenomics, gage, GenomicAlignments, GenomicRanges, glmGamPoi, HiCDCPlus, IHW, InteractiveComplexHeatmap, JctSeqData, miRmine, OPWeight, PCAtools, phyloseq, progeny, PROPER, recount, RegParallel, RUVSeq, scran, Single.mTEC.Transcriptomes, subSeq, SummarizedBenchmark, systemPipeShiny, TFEA.ChIP, tidybulk, ToPASeq, topconfects, tximeta, tximport, variancePartition, Wrench, zinbwave |
Links To Me |
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Build Report |
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Package Archives
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