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Bioconductor – DESeq2

 August 25, 2021

DOI: 10.18129/B9.bioc.DESeq2  

 

This package is for version 3.10 of Bioconductor;
for the stable, up-to-date release version, see
DESeq2.

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: 3.10

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], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb]

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

Citation (from within R,
enter citation("DESeq2")):

Installation

To install this package, start R (version
“3.6”) 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 1.26.0
In Bioconductor since BioC 2.12 (R-3.0) (7 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, Hmisc, Rcpp (>= 0.11.0)
LinkingTo Rcpp, RcppArmadillo
Suggests testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, IHW, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, pasilla(>= 0.2.10)
SystemRequirements
Enhances
URL github.com/mikelove/DESeq2
Depends On Me DChIPRep, DEWSeq, DEXSeq, FourCSeq, rgsepd, rnaseqDTU, rnaseqGene, TCC, XBSeq
Imports Me anamiR, Anaquin, animalcules, anota2seq, BloodCancerMultiOmics2017, circRNAprofiler, consensusDE, coseq, countsimQC, DaMiRseq, debrowser, DEComplexDisease, DEFormats, DEGreport, deltaCaptureC, DEsubs, DiffBind, eegc, ERSSA, FourCSeq, GDCRNATools, GenoGAM, HTSFilter, icetea, ideal, IHWpaper, ImpulseDE2, INSPEcT, IntEREst, isomiRs, JunctionSeq, kissDE, MLSeq, muscat, NBAMSeq, ORFik, OUTRIDER, PathoStat, pcaExplorer, PowerExplorer, recountWorkflow, regionReport, ReportingTools, Rmmquant, RNASeqR, scBFA, singleCellTK, SNPhood, srnadiff, systemPipeR, TimeSeriesExperiment, vidger
Suggests Me apeglm, biobroom, BiocGenerics, BioCor, BiocSet, CAGEr, CAGEWorkflow, compcodeR, curatedAdipoChIP, curatedAdipoRNA, derfinder, diffloop, EnhancedVolcano, fishpond, gage, GenomicAlignments, GenomicRanges, Glimma, IHW, JctSeqData, miRmine, OPWeight, phyloseq, progeny, recount, RegParallel, RUVSeq, scran, Single.mTEC.Transcriptomes, subSeq, SummarizedBenchmark, TFEA.ChIP, ToPASeq, topconfects, tximeta, tximport, variancePartition, Wrench, zinbwave
Links To Me
Build Report  

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package in your R session.

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