edgeR
Empirical Analysis of Digital Gene Expression Data in R
Bioconductor version: 3.23 · Package version: 4.10.5
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("edgeR")Details
| Maintainer | Yunshun Chen <yuchen@wehi.edu.au>, Gordon Smyth <smyth@wehi.edu.au>, Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>, Mark Robinson <mark.robinson@imls.uzh.ch> |
| 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 |
| License | GPL (>=2) |
| URL | https://bioinf.wehi.edu.au/edgeR/, https://bioconductor.org/packages/edgeR |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| 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 |
| Package Short Url | https://bioconductor.org/packages/edgeR/ |
Citation
From within R, enter citation("edgeR"):
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. edgeR: Empirical Analysis of Digital Gene Expression Data in R. doi:10.18129/B9.bioc.edgeR, R package version 4.10.5, https://bioconductor.org/packages/edgeR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | edgeR_4.10.5.tar.gz |
| Windows binary (x86_64) | edgeR_4.10.5.zip |
| macOS binary (arm64) | edgeR_4.10.5.tgz |
| macOS binary (x86_64) | edgeR_4.10.5.tgz |
Dependencies
Depends: R (>= 3.6.0), limma (>= 3.63.6)
Imports: methods, graphics, stats, utils, locfit
Suggests: jsonlite, knitr, Matrix, nanoparquet, readr, rhdf5, SeuratObject, splines, AnnotationDbi, Biobase, BiocStyle, org.Hs.eg.db, S4Vectors, SummarizedExperiment
Reverse dependencies
Depends On Me (17): ASpli, babel, BALLI, BioInsight, EGSEA123, IntEREst, methylMnM, miloR, octad, ReactomeGSA.data, RNAseq123, rnaseqDTU, RnaSeqGeneEdgeRQL, RnaSeqSampleSizeData, RUVSeq, TCC, tRanslatome
Imports Me (150): affycoretools, aIc, anota2seq, ATACseqQC, autonomics, AWFisher, BatchQC, baySeq, beer, benchdamic, BioQC, BreastSubtypeR, broadSeq, censcyt, ChromSCape, cinaR, circRNAprofiler, CleanUpRNAseq, clusterExperiment, CNVRanger, compcodeR, CoreMicrobiomeR, coseq, countsimQC, cpam, csaw, cypress, DaMiRseq, Damsel, debrowser, DeeDeeExperiment, DEFormats, DEGreport, DESpace, DEsubs, diffcyt, diffHic, diffUTR, diffwrap, dinoR, DMRcate, doseR, dreamlet, DRIMSeq, DropletUtils, DspikeIn, easyRNASeq, EGSEA, eisaR, emtdata, EnrichmentBrowser, erccdashboard, ERSSA, ExpHunterSuite, extraChIPs, GDCRNATools, GenomicPlot, GEOexplorer, gg4way, gINTomics, Glimma, GSEABenchmarkeR, hermes, hicream, HTSCluster, HTSFilter, icetea, idiffomix, infercnv, influential, iSEEde, IsoformSwitchAnalyzeR, KnowSeq, Maaslin2, markeR, mastR, MEB, MEDIPS, MetaDICT, metaseqR2, microbial, MIRit, MLSeq, mobileRNA, MOSim, Motif2Site, msgbsR, msmsTests, multiHiCcompare, muscat, mutscan, netZooR, pathdb, PathoStat, phantasus, PhIPData, ppcseq, PRONE, PROPER, psichomics, RCM, RCPA, recountWorkflow, regsplice, ReportingTools, RFLOMICS, RNAseqCovarImpute, RnaSeqSampleSize, ROSeq, Rvisdiff, saseR, scCB2, scde, scone, scran, ScreenR, SEtools, shinyDSP, SIMD, simPIC, singscore, SpaNorm, sparrow, spatialHeatmap, spatialLIBD, speckle, splatter, SPsimSeq, srnadiff, ssizeRNA, sSNAPPY, standR, STATegRa, Statial, SurfR, sva, TBSignatureProfiler, TCseq, tradeSeq, TransProR, treeclimbR, treekoR, TSGS, tweeDEseq, vidger, VISTA, xcore, XYomics, yarn, zinbwave
Suggests Me (74): ABSSeq, biobroom, CAGEWorkflow, chipseqDB, ClassifyR, cqn, cydar, dcanr, dearseq, DEScan2, DGEobj, DGEobj.utils, DiffBind, DiPALM, dittoSeq, DSS, easybio, easyreporting, EDASeq, gage, gCrisprTools, GenomicAlignments, GenomicRanges, GeoTcgaData, ggpicrust2, glmGamPoi, glmmSeq, goseq, groHMM, GSAR, GSVA, ideal, inDAGO, iSEEpathways, iSEEu, leeBamViews, lemur, MiscMetabar, missMethyl, MoonlightR, multiMiR, palasso, pctax, pmartR, raer, recount, regionReport, RFGeneRank, ribosomeProfilingQC, satuRn, scider, SeqGate, seqgendiff, seqwrap, SIBERG, signifinder, SpliceWiz, stageR, subSeq, systemPipeR, TCGAbiolinks, TFEA.ChIP, tidybulk, tidyexposomics, topconfects, transmogR, tximeta, tximport, variancePartition, volcano3D, weitrix, Wrench, zenith, zFPKM