DOI: 10.18129/B9.bioc.edgeR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see edgeR.

Empirical Analysis of Digital Gene Expression Data in R

Bioconductor version: 3.16

Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce read counts, including ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE and CAGE.

Author: Yunshun Chen, Aaron TL Lun, Davis J McCarthy, 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>

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biocViews AlternativeSplicing, BatchEffect, Bayesian, BiomedicalInformatics, CellBiology, ChIPSeq, Clustering, Coverage, DNAMethylation, DifferentialExpression, DifferentialMethylation, DifferentialSplicing, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, MultipleComparison, Normalization, Pathways, QualityControl, RNASeq, Regression, SAGE, Sequencing, Software, SystemsBiology, TimeCourse, Transcription, Transcriptomics
Version 3.40.2
In Bioconductor since BioC 2.3 (R-2.8) (14.5 years)
License GPL (>=2)
Depends R (>= 3.6.0), limma(>= 3.41.5)
Imports methods, graphics, stats, utils, locfit, Rcpp
LinkingTo Rcpp
Suggests jsonlite, readr, rhdf5, splines, Biobase, AnnotationDbi, SummarizedExperiment, org.Hs.eg.db
SystemRequirements C++11
URL http://bioinf.wehi.edu.au/edgeR https://bioconductor.org/packages/edgeR
Depends On Me ASpli, EGSEA123, IntEREst, methylMnM, miloR, octad, ReactomeGSA.data, RNAseq123, rnaseqDTU, RnaSeqGeneEdgeRQL, RNASeqR, RnaSeqSampleSizeData, RUVSeq, TCC, tRanslatome
Imports Me affycoretools, anota2seq, ArrayExpressHTS, ATACseqQC, autonomics, AWFisher, baySeq, beer, benchdamic, BioQC, censcyt, ChromSCape, circRNAprofiler, clusterExperiment, CNVRanger, compcodeR, consensusDE, coseq, countsimQC, crossmeta, csaw, DaMiRseq, dce, debrowser, DEComplexDisease, DEFormats, DEGreport, DEsubs, diffcyt, diffHic, diffUTR, DMRcate, doseR, DRIMSeq, DropletUtils, easyRNASeq, eegc, EGSEA, eisaR, emtdata, EnrichmentBrowser, erccdashboard, ERSSA, ExpHunterSuite, extraChIPs, GDCRNATools, Glimma, GSEABenchmarkeR, hermes, HTSFilter, icetea, infercnv, IsoformSwitchAnalyzeR, KnowSeq, Maaslin2, MEDIPS, metaseqR2, microbiomeMarker, MIGSA, MLSeq, moanin, Motif2Site, msgbsR, msmsTests, multiHiCcompare, muscat, NBSplice, PathoStat, PhIPData, ppcseq, PROPER, psichomics, RCM, recountWorkflow, regsplice, Repitools, ReportingTools, RnaSeqSampleSize, ROSeq, scCB2, scde, scone, scran, ScreenR, SEtools, SIMD, SingleCellSignalR, singscore, SingscoreAMLMutations, sparrow, spatialHeatmap, spatialLIBD, splatter, SPsimSeq, srnadiff, sSNAPPY, standR, STATegRa, sva, TBSignatureProfiler, TCseq, TimeSeriesExperiment, tradeSeq, treekoR, tweeDEseq, vidger, xcore, yarn, zinbwave
Suggests Me ABSSeq, bigPint, biobroom, CAGEWorkflow, chipseqDB, ClassifyR, cqn, cydar, dcanr, dearseq, DEScan2, dittoSeq, easyreporting, EDASeq, gage, gCrisprTools, GenomicAlignments, GenomicRanges, glmGamPoi, goseq, groHMM, GSAR, GSVA, ideal, iSEEu, leeBamViews, missMethyl, multiMiR, recount, regionReport, ribosomeProfilingQC, satuRn, SeqGate, signifinder, SpliceWiz, stageR, subSeq, SummarizedBenchmark, systemPipeR, TCGAbiolinks, tidybulk, topconfects, tximeta, tximport, variancePartition, weitrix, Wrench, zenith, zFPKM
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