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DOI: 10.18129/B9.bioc.edgeR    

This is the development version of edgeR; for the stable release version, see edgeR.

Empirical Analysis of Digital Gene Expression Data in R

Bioconductor version: Development (3.7)

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 counts, including ChIP-seq, Bisulfite-seq, SAGE and CAGE.

Author: Yunshun Chen <yuchen at>, Aaron Lun <alun at>, Davis McCarthy <dmccarthy at>, Xiaobei Zhou <xiaobei.zhou at>, Mark Robinson <mark.robinson at>, Gordon Smyth <smyth at>

Maintainer: Yunshun Chen <yuchen at>, Aaron Lun <alun at>, Mark Robinson <mark.robinson at>, Davis McCarthy <dmccarthy at>, Gordon Smyth <smyth at>

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PDF edgeR Vignette
PDF edgeRUsersGuide.pdf
PDF   Reference Manual
Text   NEWS


biocViews AlternativeSplicing, BatchEffect, Bayesian, ChIPSeq, Clustering, Coverage, DNAMethylation, DifferentialExpression, DifferentialMethylation, DifferentialSplicing, GeneExpression, GeneSetEnrichment, Genetics, MultipleComparison, Normalization, Pathways, QualityControl, RNASeq, Regression, SAGE, Sequencing, Software, TimeCourse, Transcription
Version 3.21.6
In Bioconductor since BioC 2.3 (R-2.8) (9.5 years)
License GPL (>=2)
Depends R (>= 2.15.0), limma(>= 3.34.5)
Imports graphics, stats, utils, methods, locfit, Rcpp
LinkingTo Rcpp
Suggests AnnotationDbi,, splines
SystemRequirements C++11
Depends On Me ASpli, DBChIP, EDDA, IntEREst, manta, methylMnM, MLSeq, RnaSeqSampleSizeData, RUVSeq, samExploreR, TCC, tRanslatome
Imports Me affycoretools, ampliQueso, anota2seq, ArrayExpressHTS, baySeq, compcodeR, coseq, csaw, debrowser, DEFormats, DEGreport, DEsubs, DiffBind, diffHic, diffloop, DRIMSeq, DropletUtils, easyRNASeq, EBSEA, EDDA, eegc, EGSEA, EnrichmentBrowser, erccdashboard, Glimma, HTSFilter, IsoformSwitchAnalyzeR, MEDIPS, metaseqR, MIGSA, msgbsR, msmsTests, PathoStat, PROPER, psichomics, regsplice, Repitools, ReportingTools, rnaSeqMap, RnaSeqSampleSize, scater, scde, scone, scran, splatter, STATegRa, SVAPLSseq, systemPipeR, TCGAbiolinks, TCseq, tweeDEseq, yarn, zinbwave
Suggests Me ABSSeq, biobroom, BitSeq, ClassifyR, clonotypeR, cqn, cydar, EDASeq, gage, gCrisprTools, GenomicAlignments, GenomicRanges, goseq, groHMM, GSAR, GSVA, ideal, JctSeqData, leeBamViews, missMethyl, multiMiR, regionReport, SSPA, stageR, subSeq, tximport, variancePartition, zFPKM
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