Package: edgeR 4.3.4

Yunshun Chen

edgeR: Empirical Analysis of Digital Gene Expression Data in R

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.

Authors:Yunshun Chen, Aaron TL Lun, Davis J McCarthy, Lizhong Chen, Pedro Baldoni, Matthew E Ritchie, Belinda Phipson, Yifang Hu, Xiaobei Zhou, Mark D Robinson, Gordon K Smyth

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NEWS

# Install 'edgeR' in R:
install.packages('edgeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3

On BioConductor:edgeR-4.3.0(bioc 3.20)edgeR-4.2.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

252 exports 8.65 score 5 dependencies 279 dependents 6.6k mentions

Last updated 2 months agofrom:e7f599a42f

Exports:[.CompressedMatrix[.DGEExact[.DGEGLM[.DGEList[.DGELRT[.TopTags[<-.CompressedMatrixaddPriorCountadjustedProfileLikas.data.frame.DGEExactas.data.frame.DGEGLMas.data.frame.DGEListas.data.frame.DGELRTas.data.frame.TopTagsas.matrix.CompressedMatrixas.matrix.DGEGLMas.matrix.DGEListaveLogCPMaveLogCPM.defaultaveLogCPM.DGEGLMaveLogCPM.DGEListaveLogCPM.SummarizedExperimentbinMeanVarbinomTestcalcNormFactorscalcNormFactors.defaultcalcNormFactors.DGEListcalcNormFactors.SummarizedExperimentcalcNormOffsetsforChIPcamera.DGEGLMcamera.DGEListcameraPR.DGELRTcatchKallistocatchRSEMcatchSalmoncbind.CompressedMatrixcbind.DGEListcommonCondLogLikDerDeltacondLogLikDerDeltacondLogLikDerSizecpmcpm.defaultcpm.DGEGLMcpm.DGEListcpm.DGELRTcpm.SummarizedExperimentcpmByGroupcpmByGroup.defaultcpmByGroup.DGEListcpmByGroup.SummarizedExperimentcutWithMinNdecideTests.DGEExactdecideTests.DGELRTdecideTestsDGEdesignAsFactorDGEListDGEList.data.frameDGEList.defaultdiffSpliceDGEdim.CompressedMatrixdim.DGEExactdim.DGEGLMdim.DGEListdim.DGELRTdim.TopTagsdimnames.DGEExactdimnames.DGEGLMdimnames.DGEListdimnames.DGELRTdimnames.TopTagsdimnames<-.DGEExactdimnames<-.DGEGLMdimnames<-.DGEListdimnames<-.DGELRTdispBinTrenddispCoxReiddispCoxReidInterpolateTagwisedispCoxReidPowerTrenddispCoxReidSplineTrenddispDeviancedispPearsondropEmptyLevelsedgeRUsersGuideequalizeLibSizesequalizeLibSizes.defaultequalizeLibSizes.DGEListestimateCommonDispestimateCommonDisp.defaultestimateCommonDisp.DGEListestimateDispestimateDisp.defaultestimateDisp.DGEListestimateDisp.SummarizedExperimentestimateExonGenewiseDispestimateGLMCommonDispestimateGLMCommonDisp.defaultestimateGLMCommonDisp.DGEListestimateGLMRobustDispestimateGLMTagwiseDispestimateGLMTagwiseDisp.defaultestimateGLMTagwiseDisp.DGEListestimateGLMTrendedDispestimateGLMTrendedDisp.defaultestimateGLMTrendedDisp.DGEListestimateTagwiseDispestimateTagwiseDisp.defaultestimateTagwiseDisp.DGEListestimateTrendedDispestimateTrendedDisp.defaultestimateTrendedDisp.DGEListexactTestexactTestBetaApproxexactTestByDevianceexactTestBySmallPexactTestDoubleTailexpandAsMatrixfeatureCounts2DGEListfilterByExprfilterByExpr.defaultfilterByExpr.DGEListfilterByExpr.SummarizedExperimentfry.DGEGLMfry.DGEListgetCountsgetDispersiongetNormLibSizesgetNormLibSizes.defaultgetNormLibSizes.DGEGLMgetNormLibSizes.DGEListgetNormLibSizes.DGELRTgetOffsetgetPriorNginiglmFitglmFit.defaultglmFit.DGEListglmFit.SummarizedExperimentglmLRTglmQLFitglmQLFit.defaultglmQLFit.DGEListglmQLFit.SummarizedExperimentglmQLFTestglmTreatgoana.DGEExactgoana.DGELRTgofgoodTuringgoodTuringPlotgoodTuringProportionshead.DGEExacthead.DGEGLMhead.DGEListhead.DGELRThead.TopTagskegga.DGEExactkegga.DGELRTlength.CompressedMatrixlocfitByColloessByColmakeCompressedMatrixmaPlotmaximizeInterpolantmaximizeQuadraticmglmLevenbergmglmOneGroupmglmOneWaymodelMatrixMethmovingAverageByColmroast.DGEGLMmroast.DGEListnbinomDeviancenbinomUnitDeviancenearestReftoXnearestTSSnormalizeChIPtoInputnormLibSizesnormLibSizes.defaultnormLibSizes.DGEListnormLibSizes.SummarizedExperimentOps.CompressedMatrixplotBCVplotExonUsageplotMD.DGEExactplotMD.DGEGLMplotMD.DGEListplotMD.DGELRTplotMD.SummarizedExperimentplotMDS.DGEListplotMDS.SummarizedExperimentplotMeanVarplotMeanVar2plotQLDispplotSmearplotSpliceDGEpredFCpredFC.defaultpredFC.DGEListpredFC.SummarizedExperimentprocessAmpliconsq2qnbinomq2qpoisrbind.CompressedMatrixrbind.DGEListread10XreadBismark2DGEreadDGEroast.DGEGLMroast.DGEListromer.DGEGLMromer.DGEListrowsum.DGEListrowsum.SummarizedExperimentrpkmrpkm.defaultrpkm.DGEGLMrpkm.DGEListrpkm.DGELRTrpkm.SummarizedExperimentrpkmByGrouprpkmByGroup.defaultrpkmByGroup.DGEListrpkmByGroup.SummarizedExperimentscaleOffsetscaleOffset.defaultscaleOffset.DGEListSE2DGEListSeurat2PBshowspliceVariantssplitIntoGroupssplitIntoGroups.defaultsplitIntoGroups.DGEListsplitIntoGroupsPseudosumTechRepssumTechReps.defaultsumTechReps.DGEListsumTechReps.SummarizedExperimentsystematicSubsettail.DGEExacttail.DGEGLMtail.DGEListtail.DGELRTtail.TopTagsthinCountstopSpliceDGEtopTagsvalidDGEListvoomLmFitweightedCondLogLikDerDeltaWLEBzscoreNBinom

Dependencies:latticelimmalocfitRcppstatmod

A brief introduction to edgeR

Rendered fromintro.Rmdusingknitr::rmarkdownon May 13 2024.

Last update: 2024-01-28
Started: 2023-06-21

edgeR User's Guide

Rendered fromedgeRUsersGuide.Rnwusingutils::Sweaveon May 13 2024.

Last update: 2023-06-20
Started: 2023-06-20

Readme and manuals

Help Manual

Help pageTopics
Empirical analysis of digital gene expression data in RedgeR-package edgeR
Add a prior countaddPriorCount
Adjusted Profile Likelihood for the Negative Binomial Dispersion ParameteradjustedProfileLik
Collapse TopTags or Other edgeR Object to a Data Frameas.data.frame.DGEExact as.data.frame.DGEGLM as.data.frame.DGEList as.data.frame.DGELRT as.data.frame.TopTags
Collapse a DGEList or DGEGLM Object to a Matrixas.matrix.DGEGLM as.matrix.DGEList
Average Log Counts Per MillionaveLogCPM aveLogCPM.default aveLogCPM.DGEGLM aveLogCPM.DGEList aveLogCPM.SummarizedExperiment
Exact Binomial Tests for Comparing Two Digital LibrariesbinomTest
Competitive Gene Set Tests for Digital Gene Expression Datacamera.DGEGLM camera.DGEList cameraPR.DGELRT
Process Salmon, kallisto or RSEM Transcript OutputcatchKallisto catchRSEM catchSalmon
Combine DGEList Objectscbind cbind.DGEList rbind.DGEList
Conditional Log-Likelihoods in Terms of DeltacommonCondLogLikDerDelta
Conditional Log-Likelihood of the Dispersion for a Single Group of Replicate LibrariescondLogLikDerDelta condLogLikDerSize
Counts per Million or Reads per Kilobase per Millioncpm cpm.default cpm.DGEGLM cpm.DGEList cpm.DGELRT cpm.SummarizedExperiment cpmByGroup cpmByGroup.default cpmByGroup.DGEList cpmByGroup.SummarizedExperiment rpkm rpkm.default rpkm.DGEGLM rpkm.DGEList rpkm.DGELRT rpkm.SummarizedExperiment rpkmByGroup rpkmByGroup.default rpkmByGroup.DGEList rpkmByGroup.SummarizedExperiment
Cut Numeric Vector Into Non-empty IntervalscutWithMinN
Multiple Testing Across Genes and ContrastsdecideTests.DGEExact decideTests.DGELRT decideTestsDGE
differential expression of Digital Gene Expression data - classDGEExact-class show,DGEExact-method
Digital Gene Expression Generalized Linear Model results - classDGEGLM-class show,DGEGLM-method
Create a DGEList objectDGEList DGEList.data.frame DGEList.default
Digital Gene Expression data - classDGEList-class
Digital Gene Expression Likelihood Ratio Test data and results - classDGELRT-class show,DGELRT-method
Test for Differential Exon UsagediffSpliceDGE
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Objectdim.DGEExact dim.DGEGLM dim.DGEList dim.DGELRT dim.TopTags
Retrieve the Dimension Names of a DGE Objectdimnames.DGEExact dimnames.DGEGLM dimnames.DGEList dimnames.DGELRT dimnames.TopTags dimnames<-.DGEExact dimnames<-.DGEGLM dimnames<-.DGEList dimnames<-.DGELRT
Estimate Dispersion Trend by Binning for NB GLMsdispBinTrend
Estimate Common Dispersion for Negative Binomial GLMsdispCoxReid dispDeviance dispPearson
Estimate Genewise Dispersion for Negative Binomial GLMs by Cox-Reid Adjusted Profile LikelihooddispCoxReidInterpolateTagwise
Estimate Dispersion Trend for Negative Binomial GLMsdispCoxReidPowerTrend dispCoxReidSplineTrend
Drop Levels of a Factor that Never OccurdropEmptyLevels
View edgeR User's GuideedgeRUsersGuide
Equalize Library Sizes by Quantile-to-Quantile NormalizationequalizeLibSizes equalizeLibSizes.default equalizeLibSizes.DGEList
Estimate Common Negative Binomial Dispersion by Conditional Maximum LikelihoodestimateCommonDisp estimateCommonDisp.default estimateCommonDisp.DGEList
Estimate Common, Trended and Tagwise Negative Binomial dispersions by weighted likelihood empirical BayesestimateDisp estimateDisp.default estimateDisp.DGEList estimateDisp.SummarizedExperiment
Estimate Genewise Dispersions from Exon-Level Count DataestimateExonGenewiseDisp
Estimate Common Dispersion for Negative Binomial GLMsestimateGLMCommonDisp estimateGLMCommonDisp.default estimateGLMCommonDisp.DGEList
Empirical Robust Bayes Tagwise Dispersions for Negative Binomial GLMs using Observation WeightsestimateGLMRobustDisp
Empirical Bayes Tagwise Dispersions for Negative Binomial GLMsestimateGLMTagwiseDisp estimateGLMTagwiseDisp.default estimateGLMTagwiseDisp.DGEList
Estimate Trended Dispersion for Negative Binomial GLMsestimateGLMTrendedDisp estimateGLMTrendedDisp.default estimateGLMTrendedDisp.DGEList
Estimate Empirical Bayes Tagwise Dispersion ValuesestimateTagwiseDisp estimateTagwiseDisp.default estimateTagwiseDisp.DGEList
Estimate Empirical Bayes Trended Dispersion ValuesestimateTrendedDisp estimateTrendedDisp.default estimateTrendedDisp.DGEList
Exact Tests for Differences between Two Groups of Negative-Binomial CountsexactTest exactTestBetaApprox exactTestByDeviance exactTestBySmallP exactTestDoubleTail
expandAsMatrixexpandAsMatrix
Convert featureCounts object to a DGEListfeatureCounts2DGEList
Filter Genes By Expression LevelfilterByExpr filterByExpr.default filterByExpr.DGEList filterByExpr.SummarizedExperiment
Extract Specified Component of a DGEList ObjectgetCounts getDispersion getOffset
Effective Library SizesgetNormLibSizes getNormLibSizes.default getNormLibSizes.DGEGLM getNormLibSizes.DGEList getNormLibSizes.DGELRT
Get a Recommended Value for Prior N from DGEList ObjectgetPriorN
Gini dispersion indexgini
Genewise Negative Binomial Generalized Linear ModelsglmFit glmFit.default glmFit.DGEList glmFit.SummarizedExperiment
Genewise Likelihood Ratio TestsglmLRT
Genewise Negative Binomial Generalized Linear Models with Quasi-Dispersion EstimationglmQLFit glmQLFit.default glmQLFit.DGEList glmQLFit.SummarizedExperiment
Quasi-Likelihood F-TestsglmQLFTest
Test for Differential Expression Relative to a ThresholdglmTreat
Gene Ontology or KEGG Analysis of Differentially Expressed Genesgoana.DGEExact goana.DGELRT kegga.DGEExact kegga.DGELRT
Goodness of Fit Tests for Multiple GLM Fitsgof
Good-Turing Frequency EstimationgoodTuring goodTuringPlot goodTuringProportions
Return the First to Last Part of a Data Objecthead.DGEExact head.DGEGLM head.DGEList head.DGELRT head.TopTags tail.DGEExact tail.DGEGLM tail.DGEList tail.DGELRT tail.TopTags
Locally Weighted Mean By ColumnlocfitByCol loessByCol
makeCompressedMatrixas.matrix.CompressedMatrix cbind.CompressedMatrix CompressedMatrix CompressedMatrix-class dim.CompressedMatrix length.CompressedMatrix makeCompressedMatrix Ops.CompressedMatrix rbind.CompressedMatrix [.CompressedMatrix [<-.CompressedMatrix
Plots Log-Fold Change versus Log-Concentration (or, M versus A) for Count DatamaPlot
Maximize a function given a table of values by spline interpolation.maximizeInterpolant
Maximize a function given a table of values by quadratic interpolation.maximizeQuadratic
Explore the Mean-Variance Relationship for DGE DatabinMeanVar plotMeanVar
Fit Negative Binomial Generalized Linear Models to Multiple Response Vectors: Low Level FunctionsdesignAsFactor mglm mglmLevenberg mglmOneGroup mglmOneWay
Construct Design Matrix for edgeR Analysis of Methylation Count DatamodelMatrixMeth
Moving Average Smoother of Matrix ColumnsmovingAverageByCol
Negative Binomial DeviancenbinomDeviance
Negative Binomial Unit DeviancenbinomUnitDeviance
Find Nearest Element of Reference for each Element of XnearestReftoX
Find Nearest Transcriptional Start SitenearestTSS
Normalize ChIP-Seq Read Counts to Input and Test for EnrichmentcalcNormOffsetsforChIP normalizeChIPtoInput
Normalize Library SizescalcNormFactors calcNormFactors.default calcNormFactors.DGEList calcNormFactors.SummarizedExperiment normLibSizes normLibSizes.default normLibSizes.DGEList normLibSizes.SummarizedExperiment
Plot Biological Coefficient of VariationplotBCV
Create a Plot of Exon Usage from Exon-Level Count DataplotExonUsage
Mean-Difference Plot of Count DataplotMD.DGEExact plotMD.DGEGLM plotMD.DGEList plotMD.DGELRT plotMD.SummarizedExperiment
Multidimensional scaling plot of distances between digital gene expression profilesplotMDS.DGEList plotMDS.SummarizedExperiment
Plot Mean-Variance Relationship in DGE Data Using Standardized ResidualsplotMeanVar2
Plot the quasi-likelihood dispersionplotQLDisp
Smear plotplotSmear
Differential splicing plotplotSpliceDGE
Predictive log-fold changespredFC predFC.default predFC.DGEList predFC.SummarizedExperiment
Process FASTQ files from pooled genetic sequencing screensprocessAmplicons
Quantile to Quantile Mapping between Negative-Binomial Distributionsq2qnbinom q2qpois
Read 10X Genomics Filesread10X
Read Bismark Coverage FilesreadBismark2DGE
Read and Merge a Set of Files Containing Count DatareadDGE
Self-contained Gene Set Tests for Digital Gene Expression Datafry.DGEGLM mroast.DGEGLM roast.DGEGLM
Self-contained Gene Set Tests for Digital Gene Expression Datafry.DGEList mroast.DGEList roast.DGEList
Rotation Gene Set Enrichment for Digital Gene Expression Dataromer.DGEGLM
Rotation Gene Set Enrichment for Digital Gene Expression Dataromer.DGEList
Sum Over Groups of Genesrowsum.DGEList rowsum.SummarizedExperiment
Scale offsetsscaleOffset scaleOffset.default scaleOffset.DGEList
SummarizedExperiment to DGEListSE2DGEList
Seurat or SeuratObject class object to pseudo-bulk DGEListSeurat2PB
Identify Genes with Splice VariantsspliceVariants
Split the Counts or Pseudocounts from a DGEList Object According To GroupsplitIntoGroups splitIntoGroups.default splitIntoGroups.DGEList splitIntoGroupsPseudo
Subset DGEList, DGEGLM, DGEExact and DGELRT Objectssubsetting [.DGEExact [.DGEGLM [.DGEList [.DGELRT [.TopTags
Sum Over Replicate SamplessumTechReps sumTechReps.default sumTechReps.DGEList sumTechReps.SummarizedExperiment
Take a systematic subset of indices.systematicSubset
Binomial or Multinomial Thinning of CountsthinCounts
Top table of differentially spliced genes or exonstopSpliceDGE
Table of the Top Differentially Expressed Genes/Tagsshow,TopTags-method topTags TopTags-class
Check for Valid DGEList objectvalidDGEList
Apply voom-lmFit Pipeline While Accounting for Loss of Residual DF Due to Exact ZerosvoomLmFit
Weighted Conditional Log-Likelihood in Terms of DeltaweightedCondLogLikDerDelta
Weighted Likelihood Empirical BayesWLEB
Z-score Equivalents of Negative Binomial DeviatezscoreNBinom