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Bioconductor - edgeR

edgeR

This is the released version of edgeR; for the devel version, see edgeR.

Empirical Analysis of Digital Gene Expression Data in R

Bioconductor version: Release (3.21)

Differential expression analysis of sequence count data. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models, quasi-likelihood, and gene set enrichment. Can perform differential analyses of any type of omics data that produces read counts, including RNA-seq, ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE, CAGE, metabolomics, or proteomics spectral counts. RNA-seq analyses can be conducted at the gene or isoform level, and tests can be conducted for differential exon or transcript usage.

Author: Yunshun Chen, Lizhong Chen, Aaron TL Lun, Davis J McCarthy, Pedro Baldoni, Matthew E Ritchie, Belinda Phipson, Yifang Hu, Xiaobei Zhou, Mark D Robinson, Gordon K Smyth

Maintainer: Yunshun Chen <yuchen at wehi.edu.au>, Gordon Smyth <smyth at wehi.edu.au>, Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>, Mark Robinson <mark.robinson at imls.uzh.ch>

Citation (from within R, enter citation("edgeR")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("edgeR")

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("edgeR")

Details biocViews AlternativeSplicing, BatchEffect, Bayesian, BiomedicalInformatics, CellBiology, ChIPSeq, Clustering, Coverage, DNAMethylation, DifferentialExpression, DifferentialMethylation, DifferentialSplicing, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, MultipleComparison, Normalization, Pathways, Proteomics, QualityControl, RNASeq, Regression, SAGE, Sequencing, SingleCell, Software, SystemsBiology, TimeCourse, Transcription, Transcriptomics Version 4.6.3 In Bioconductor since BioC 2.3 (R-2.8) (16.5 years) License GPL (>=2) Depends R (>= 3.6.0), limma(>= 3.63.6) Imports methods, graphics, stats, utils, locfit System Requirements URL https://bioinf.wehi.edu.au/edgeR/ https://bioconductor.org/packages/edgeR See More Suggests arrow, jsonlite, knitr, Matrix, readr, rhdf5, SeuratObject, splines, AnnotationDbi, Biobase, BiocStyle, org.Hs.eg.db, SummarizedExperiment Linking To Enhances Depends On Me ASpli, IntEREst, methylMnM, miloR, octad, RUVSeq, TCC, tRanslatome, ReactomeGSA.data, EGSEA123, RNAseq123, rnaseqDTU, RnaSeqGeneEdgeRQL, csawBook, OSCA.advanced, OSCA.multisample, OSCA.workflows, babel, BALLI, BioInsight, SCdeconR Imports Me affycoretools, ATACseqQC, autonomics, AWFisher, baySeq, beer, benchdamic, BioQC, broadSeq, censcyt, ChromSCape, circRNAprofiler, CleanUpRNAseq, clusterExperiment, CNVRanger, compcodeR, consensusDE, coseq, countsimQC, csaw, cypress, DaMiRseq, Damsel, dce, debrowser, DEFormats, DEGreport, DESpace, DEsubs, diffcyt, diffHic, diffUTR, dinoR, DMRcate, doseR, dreamlet, DRIMSeq, DropletUtils, easyRNASeq, EGSEA, eisaR, EnrichmentBrowser, erccdashboard, ERSSA, extraChIPs, GDCRNATools, GenomicPlot, GEOexplorer, gg4way, gINTomics, Glimma, GSEABenchmarkeR, hermes, HTSFilter, icetea, infercnv, iSEEde, IsoformSwitchAnalyzeR, KnowSeq, Maaslin2, mastR, MEB, MEDIPS, metaseqR2, MIRit, MLSeq, moanin, mobileRNA, MOSim, Motif2Site, msgbsR, msmsTests, multiHiCcompare, muscat, PathoStat, phantasus, PhIPData, ppcseq, PRONE, PROPER, psichomics, RCM, regsplice, Repitools, RFLOMICS, RNAseqCovarImpute, ROSeq, Rvisdiff, saseR, scCB2, scde, scone, scran, ScreenR, SEtools, shinyDSP, SIMD, SingleCellSignalR, singscore, SpaNorm, sparrow, spatialHeatmap, speckle, splatter, SPsimSeq, srnadiff, sSNAPPY, standR, STATegRa, SurfR, sva, TBSignatureProfiler, TCseq, tradeSeq, treeclimbR, treekoR, tweeDEseq, vidger, xcore, yarn, zinbwave, emtdata, spatialLIBD, ExpHunterSuite, recountWorkflow, SingscoreAMLMutations, aIc, bulkAnalyseR, CAMML, CIDER, cinaR, CoreMicrobiomeR, cpam, HTSCluster, idiffomix, inDAGO, microbial, RCPA, RVA, scITD, scRNAtools, SPUTNIK, ssizeRNA, TransProR, TSGS Suggests Me ABSSeq, biobroom, ClassifyR, cqn, cydar, dcanr, dearseq, DEScan2, DiffBind, dittoSeq, DSS, easyreporting, EDASeq, gage, gCrisprTools, GenomicAlignments, GenomicRanges, GeoTcgaData, glmGamPoi, goseq, groHMM, GSAR, GSVA, ideal, iSEEpathways, iSEEu, lemur, missMethyl, MoonlightR, multiMiR, raer, recount, regionReport, ribosomeProfilingQC, satuRn, scider, SeqGate, signifinder, SpliceWiz, stageR, subSeq, systemPipeR, TCGAbiolinks, tidybulk, topconfects, transmogR, tximeta, tximport, variancePartition, weitrix, Wrench, zenith, zFPKM, leeBamViews, CAGEWorkflow, chipseqDB, DGEobj, DGEobj.utils, DiPALM, easybio, ggpicrust2, glmmSeq, MiscMetabar, palasso, pctax, pmartR, seqgendiff, SIBERG, volcano3D Links To Me Build Report Build Report Package Archives

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

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