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>

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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 3.24.3
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
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
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Source Package edgeR_3.24.3.tar.gz
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