edgeR

DOI: 10.18129/B9.bioc.edgeR    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see edgeR.

Empirical Analysis of Digital Gene Expression Data in R

Bioconductor version: 3.8

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 wehi.edu.au>, Aaron Lun <alun at wehi.edu.au>, Davis McCarthy <dmccarthy at wehi.edu.au>, Xiaobei Zhou <xiaobei.zhou at uzh.ch>, Mark Robinson <mark.robinson at imls.uzh.ch>, Gordon Smyth <smyth at wehi.edu.au>

Maintainer: Yunshun Chen <yuchen at wehi.edu.au>, Aaron Lun <alun at wehi.edu.au>, Mark Robinson <mark.robinson at imls.uzh.ch>, Davis McCarthy <dmccarthy at wehi.edu.au>, Gordon Smyth <smyth at wehi.edu.au>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

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

Details

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	3.24.3
In Bioconductor since	BioC 2.3 (R-2.8) (10.5 years)
License	GPL (>=2)
Depends	R (>= 2.15.0), limma(>= 3.34.5)
Imports	graphics, stats, utils, methods, locfit, Rcpp
LinkingTo	Rcpp
Suggests	AnnotationDbi, jsonlite, org.Hs.eg.db, readr, rhdf5, splines
SystemRequirements	C++11
Enhances
URL	http://bioinf.wehi.edu.au/edgeR
Depends On Me	ASpli, chipseqDB, DBChIP, EDDA, EGSEA123, IntEREst, manta, methylMnM, RNAseq123, rnaseqDTU, RnaSeqGeneEdgeRQL, RNASeqR, RnaSeqSampleSizeData, RUVSeq, samExploreR, simpleSingleCell, TCC, tRanslatome
Imports Me	affycoretools, ampliQueso, anota2seq, ArrayExpressHTS, baySeq, clusterExperiment, compcodeR, consensusDE, coseq, countsimQC, csaw, DaMiRseq, debrowser, DEComplexDisease, DEFormats, DEGreport, DEsubs, DiffBind, diffcyt, diffHic, diffloop, DRIMSeq, DropletUtils, easyRNASeq, EBSEA, EDDA, eegc, EGSEA, EnrichmentBrowser, erccdashboard, ERSSA, GDCRNATools, Glimma, GSEABenchmarkeR, HTSFilter, icetea, IsoformSwitchAnalyzeR, MEDIPS, metaseqR, MIGSA, MLSeq, msgbsR, msmsTests, multiHiCcompare, NBSplice, PathoStat, PROPER, psichomics, recountWorkflow, regsplice, Repitools, ReportingTools, rnaSeqMap, RnaSeqSampleSize, scde, scone, scran, SIMD, singscore, splatter, STATegRa, SVAPLSseq, systemPipeR, TCGAbiolinks, TCseq, TimeSeriesExperiment, tweeDEseq, vidger, yarn, zinbwave
Suggests Me	ABSSeq, biobroom, BitSeq, ClassifyR, clonotypeR, cqn, cydar, DEScan2, EDASeq, gage, gCrisprTools, GenomicAlignments, GenomicRanges, goseq, groHMM, GSAR, GSVA, ideal, JctSeqData, leeBamViews, missMethyl, multiMiR, regionReport, SSPA, stageR, subSeq, SummarizedBenchmark, tximport, variancePartition, Wrench, zFPKM
Links To Me
Build Report

Package Archives

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

Source Package	edgeR_3.24.3.tar.gz
Windows Binary	edgeR_3.24.3.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	edgeR_3.24.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/edgeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/edgeR
Package Short Url	http://bioconductor.org/packages/edgeR/
Package Downloads Report	Download Stats