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 counts, including ChIP-seq, SAGE and CAGE.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("edgeR")
AuthorYunshun Chen <yuchen@wehi.edu.au>, Aaron Lun <alun@wehi.edu.au>, Davis McCarthy <dmccarthy@wehi.edu.au>, Xiaobei Zhou <xiaobei.zhou@uzh.ch>, Mark Robinson <mark.robinson@imls.uzh.ch>, Gordon Smyth <smyth@wehi.edu.au>
Bioconductor views AlternativeSplicing BatchEffect Bayesian ChIPSeq Clustering Coverage DifferentialExpression DifferentialSplicing GeneExpression GeneSetEnrichment Genetics MultipleComparison Normalization QualityControl RNASeq Regression SAGE Sequencing TimeCourse Transcription
Date of publicationNone
MaintainerYunshun Chen <yuchen@wehi.edu.au>, Aaron Lun <alun@wehi.edu.au>, Mark Robinson <mark.robinson@imls.uzh.ch>, Davis McCarthy <dmccarthy@wehi.edu.au>, Gordon Smyth <smyth@wehi.edu.au>
LicenseGPL (>=2)
Version3.16.5
http://bioinf.wehi.edu.au/edgeR

View on Bioconductor

Man pages

addPriorCount: Add a prior count

adjustedProfileLik: Adjusted Profile Likelihood for the Negative Binomial...

asdataframe: Turn a TopTags Object into a Dataframe

asmatrix: Turn a DGEList Object into a Matrix

aveLogCPM: Average Log Counts Per Million

binomTest: Exact Binomial Tests for Comparing Two Digital Libraries

calcNormFactors: Calculate Normalization Factors to Align Columns of a Count...

camera.DGEList: Competitive Gene Set Test for Digital Gene Expression Data...

commonCondLogLikDerDelta: Conditional Log-Likelihoods in Terms of Delta

condLogLikDerSize: Conditional Log-Likelihood of the Dispersion for a Single...

cpm: Counts per Million or Reads per Kilobase per Million

cutWithMinN: Cut numeric vector into non-empty intervals

decidetestsDGE: Multiple Testing Across Genes and Contrasts

DGEExact-class: differential expression of Digital Gene Expression data -...

DGEGLM-class: Digital Gene Expression Generalized Linear Model results -...

DGEList: DGEList Constructor

DGEList-class: Digital Gene Expression data - class

DGELRT-class: Digital Gene Expression Likelihood Ratio Test data and...

dglmStdResid: Visualize the mean-variance relationship in DGE data using...

diffSpliceDGE: Test for Differential Exon Usage

dim: Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM,...

dimnames: Retrieve the Dimension Names of a DGE Object

dispBinTrend: Estimate Dispersion Trend by Binning for NB GLMs

dispCoxReid: Estimate Common Dispersion for Negative Binomial GLMs

dispCoxReidInterpolateTagwise: Estimate Genewise Dispersion for Negative Binomial GLMs by...

dispCoxReidSplineTrend: Estimate Dispersion Trend for Negative Binomial GLMs

dropEmptyLevels: Drop Levels of a Factor that Never Occur

edgeR-package: Empirical analysis of digital gene expression data in R

edgeRUsersGuide: View edgeR User's Guide

equalizeLibSizes: Equalize Library Sizes by Quantile-to-Quantile Normalization

estimateCommonDisp: Estimate Common Negative Binomial Dispersion by Conditional...

estimateDisp: Estimate Common, Trended and Tagwise Negative Binomial...

estimateExonGenewisedisp: Estimate Genewise Dispersions from Exon-Level Count Data

estimateGLMCommonDisp: Estimate Common Dispersion for Negative Binomial GLMs

estimateGLMRobustDisp: Empirical Robust Bayes Tagwise Dispersions for Negative...

estimateGLMTagwiseDisp: Empirical Bayes Tagwise Dispersions for Negative Binomial...

estimateGLMTrendedDisp: Estimate Trended Dispersion for Negative Binomial GLMs

estimateTagwiseDisp: Estimate Empirical Bayes Tagwise Dispersion Values

estimateTrendedDisp: Estimate Empirical Bayes Trended Dispersion Values

exactTest: Exact Tests for Differences between Two Groups of...

expandAsMatrix: expandAsMatrix

getCounts: Extract Specified Component of a DGEList Object

getPriorN: Get a Recommended Value for Prior N from DGEList Object

gini: Gini dispersion index

glmfit: Genewise Negative Binomial Generalized Linear Models

glmQLFTest: Genewise Negative Binomial Generalized Linear Models with...

glmTreat: Test for Differential Expression Relative to a Threshold

goana: Gene Ontology or KEGG Analysis of Differentially Expressed...

gof: Goodness of Fit Tests for Multiple GLM Fits

goodTuring: Good-Turing Frequency Estimation

loessByCol: Locally Weighted Mean By Column

makeCompressedMatrix: makeCompressedMatrix

maPlot: Plots Log-Fold Change versus Log-Concentration (or, M versus...

maximizeInterpolant: Maximize a function given a table of values by spline...

maximizeQuadratic: Maximize a function given a table of values by quadratic...

meanvar: Explore the mean-variance relationship for DGE data

mglm: Fit Negative Binomial Generalized Linear Model to Multiple...

movingAverageByCol: Moving Average Smoother of Matrix Columns

nbinomDeviance: Negative Binomial Deviance

normalizeChIPtoInput: Normalize ChIP-Seq Read Counts to Input and Test for...

plotBCV: Plot Biological Coefficient of Variation

plotExonUsage: Create a Plot of Exon Usage from Exon-Level Count Data

plotMD: Mean-Difference Plot of Count Data

plotMDS.DGEList: Multidimensional scaling plot of distances between digital...

plotQLDisp: Plot the quasi-likelihood dispersion

plotSmear: Smear plot

plotSpliceDGE: Differential splicing plot

predFC: Predictive log-fold changes

processAmplicons: Process raw data from pooled genetic sequencing screens

q2qnbinom: Quantile to Quantile Mapping between Negative-Binomial...

readDGE: Read and Merge a Set of Files Containing Count Data

roast.DGEList: Rotation Gene Set Tests for Digital Gene Expression Data

romer.DGEList: Rotation Gene Set Tests for Digital Gene Expression Data

scaleOffset: Scale offsets

spliceVariants: Identify Genes with Splice Variants

splitIntoGroups: Split the Counts or Pseudocounts from a DGEList Object...

subsetting: Subset DGEList, DGEGLM, DGEExact and DGELRT Objects

sumTechReps: Sum Over Replicate Samples

systematicSubset: Take a systematic subset of indices.

thinCounts: Binomial or Multinomial Thinning of Counts

topSpliceDGE: Top table of differentially spliced genes or exons

topTags: Table of the Top Differentially Expressed Tags

validDGEList: Check for Valid DGEList object

weightedCondLogLikDerDelta: Weighted Conditional Log-Likelihood in Terms of Delta

WLEB: Calculate Weighted Likelihood Empirical Bayes Estimates

zscoreNBinom: Z-score Equivalents of Negative Binomial Deviate

Functions

addPriorCount Man page
adjustedProfileLik Man page
as.data.frame.TopTags Man page
as.matrix.compressedMatrix Man page
as.matrix.DGEList Man page
aveLogCPM Man page
aveLogCPM.default Man page
aveLogCPM.DGEGLM Man page
aveLogCPM.DGEList Man page
binMeanVar Man page
binomTest Man page
calcNormFactors Man page
calcNormFactors.default Man page
calcNormFactors.DGEList Man page
calcNormOffsetsforChIP Man page
camera.DGEList Man page
commonCondLogLikDerDelta Man page
compressedMatrix Man page
[.compressedMatrix Man page
condLogLikDerDelta Man page
condLogLikDerSize Man page
cpm Man page
cpm.default Man page
cpm.DGEList Man page
cutWithMinN Man page
decideTestsDGE Man page
designAsFactor Man page
[.DGEExact Man page
DGEExact-class Man page
[.DGEGLM Man page
DGEGLM-class Man page
DGEList Man page
[.DGEList Man page
DGEList-class Man page
[.DGELRT Man page
DGELRT-class Man page
dglmStdResid Man page
diffSpliceDGE Man page
dim.DGEExact Man page
dim.DGEGLM Man page
dim.DGEList Man page
dim.DGELRT Man page
dimnames<-.DGEExact Man page
dimnames.DGEExact Man page
dimnames<-.DGEGLM Man page
dimnames.DGEGLM Man page
dimnames<-.DGEList Man page
dimnames.DGEList Man page
dimnames<-.DGELRT Man page
dimnames.DGELRT Man page
dimnames.TopTags Man page
dim.TopTags Man page
dispBinTrend Man page
dispCoxReid Man page
dispCoxReidInterpolateTagwise Man page
dispCoxReidPowerTrend Man page
dispCoxReidSplineTrend Man page
dispDeviance Man page
dispPearson Man page
dropEmptyLevels Man page
edgeR Man page
edgeR-package Man page
edgeRUsersGuide Man page
equalizeLibSizes Man page
equalizeLibSizes.default Man page
equalizeLibSizes.DGEList Man page
estimateCommonDisp Man page
estimateCommonDisp.default Man page
estimateCommonDisp.DGEList Man page
estimateDisp Man page
estimateDisp.default Man page
estimateDisp.DGEList Man page
estimateExonGenewiseDisp Man page
estimateGLMCommonDisp Man page
estimateGLMCommonDisp.default Man page
estimateGLMCommonDisp.DGEList Man page
estimateGLMRobustDisp Man page
estimateGLMTagwiseDisp Man page
estimateGLMTagwiseDisp.default Man page
estimateGLMTagwiseDisp.DGEList Man page
estimateGLMTrendedDisp Man page
estimateGLMTrendedDisp.default Man page
estimateGLMTrendedDisp.DGEList Man page
estimateTagwiseDisp Man page
estimateTagwiseDisp.default Man page
estimateTagwiseDisp.DGEList Man page
estimateTrendedDisp Man page
estimateTrendedDisp.default Man page
estimateTrendedDisp.DGEList Man page
exactTest Man page
exactTestBetaApprox Man page
exactTestByDeviance Man page
exactTestBySmallP Man page
exactTestDoubleTail Man page
expandAsMatrix Man page
fry.DGEList Man page
getCounts Man page
getDispersion Man page
getDispersions Man page
getOffset Man page
getPriorN Man page
gini Man page
glmFit Man page
glmFit.default Man page
glmFit.DGEList Man page
glmLRT Man page
glmQLFit Man page
glmQLFit.default Man page
glmQLFit.DGEList Man page
glmQLFTest Man page
glmTreat Man page
goana.DGEExact Man page
goana.DGELRT Man page
gof Man page
goodTuring Man page
goodTuringPlot Man page
goodTuringProportions Man page
kegga.DGEExact Man page
kegga.DGELRT Man page
length.DGEExact Man page
length.DGEGLM Man page
length.DGEList Man page
length.DGELRT Man page
length.TopTags Man page
locfitByCol Man page
loessByCol Man page
makeCompressedMatrix Man page
maPlot Man page
maximizeInterpolant Man page
maximizeQuadratic Man page
mglm Man page
mglmLevenberg Man page
mglmOneGroup Man page
mglmOneWay Man page
movingAverageByCol Man page
mroast.DGEList Man page
nbinomDeviance Man page
nbinomUnitDeviance Man page
normalizeChIPtoInput Man page
plotBCV Man page
plotExonUsage Man page
plotMD.DGEExact Man page
plotMD.DGEGLM Man page
plotMD.DGEList Man page
plotMD.DGELRT Man page
plotMDS.DGEList Man page
plotMeanVar Man page
plotQLDisp Man page
plotSmear Man page
plotSpliceDGE Man page
predFC Man page
predFC.default Man page
predFC.DGEList Man page
processAmplicons Man page
q2qnbinom Man page
q2qpois Man page
readDGE Man page
roast.DGEList Man page
romer.DGEList Man page
rpkm Man page
rpkm.default Man page
rpkm.DGEList Man page
scaleOffset Man page
scaleOffset.default Man page
scaleOffset.DGEList Man page
show,DGEExact-method Man page
show,DGEGLM-method Man page
show,DGELRT-method Man page
show,TopTags-method Man page
spliceVariants Man page
splitIntoGroups Man page
splitIntoGroups.default Man page
splitIntoGroups.DGEList Man page
splitIntoGroupsPseudo Man page
subsetting Man page
sumTechReps Man page
sumTechReps.default Man page
sumTechReps.DGEList Man page
systematicSubset Man page
thinCounts Man page
topSpliceDGE Man page
topTags Man page
[.TopTags Man page
TopTags-class Man page
validDGEList Man page
weightedCondLogLikDerDelta Man page
WLEB Man page
zscoreNBinom Man page

Files

DESCRIPTION
NAMESPACE
R
R/DGEList.R R/S3methods.R R/addPriorCount.R R/adjustedProfileLik.R R/aveLogCPM.R R/binomTest.R R/calcNormFactors.R R/calcNormOffsets.R R/classes.R R/commonCondLogLikDerDelta.R R/condLogLikDerDelta.R R/condLogLikDerSize.R R/cpm.R R/cutWithMinN.R R/decidetestsDGE.R R/dglmStdResid.R R/diffSpliceDGE.R R/dispBinTrend.R R/dispCoxReid.R R/dispCoxReidInterpolateTagwise.R R/dispCoxReidPowerTrend.R R/dispCoxReidSplineTrend.R R/dispDeviance.R R/dispPearson.R R/dropEmptyLevels.R R/edgeRUsersGuide.R R/equalizeLibSizes.R R/estimateCommonDisp.R R/estimateDisp.R R/estimateGLMCommonDisp.R R/estimateGLMRobustDisp.R R/estimateGLMTagwiseDisp.R R/estimateGLMTrendedDisp.R R/estimateTagwiseDisp.R R/estimateTrendedDisp.R R/exactTest.R R/exactTestBetaApprox.R R/exactTestByDeviance.R R/exactTestBySmallP.R R/exactTestDoubleTail.R R/expandAsMatrix.R R/geneset-DGEList.R R/getCounts.R R/getDispersion.R R/getOffset.R R/getPriorN.R R/gini.R R/glmQLFTest.R R/glmTreat.R R/glmfit.R R/goana.R R/gof.R R/goodTuring.R R/kegga.R R/locfitByCol.R R/loessByCol.R R/maPlot.R R/makeCompressedMatrix.R R/maximizeInterpolant.R R/maximizeQuadratic.R R/meanvar.R R/mglmLevenberg.R R/mglmOneGroup.R R/mglmOneWay.R R/movingAverageByCol.R R/nbinomDeviance.R R/normalizeChIPtoInput.R R/plotBCV.R R/plotMD.R R/plotMDS.DGEList.R R/plotSmear.R R/predFC.R R/processAmplicons.R R/q2qnbinom.R R/readDGE.R R/residDF.R R/rpkm.R R/scaleOffset.R R/spliceVariants.R R/splitIntoGroups.R R/splitIntoGroupsPseudo.R R/subsetting.R R/sumTechReps.R R/systematicSubset.R R/thinCounts.R R/topTags.R R/validDGEList.R R/weightedCondLogLikDerDelta.R R/zscoreNBinom.R R/zzz.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/edgeR.Rnw
inst/doc/edgeR.pdf
inst/doc/edgeRUsersGuide.pdf
inst/doc/index.html
man
man/DGEExact-class.Rd man/DGEGLM-class.Rd man/DGELRT-class.Rd man/DGEList-class.Rd man/DGEList.Rd man/WLEB.Rd man/addPriorCount.Rd man/adjustedProfileLik.Rd man/asdataframe.Rd man/asmatrix.Rd man/aveLogCPM.Rd man/binomTest.Rd man/calcNormFactors.Rd man/camera.DGEList.Rd man/commonCondLogLikDerDelta.Rd man/condLogLikDerSize.Rd man/cpm.Rd man/cutWithMinN.Rd man/decidetestsDGE.Rd man/dglmStdResid.Rd man/diffSpliceDGE.Rd man/dim.Rd man/dimnames.Rd man/dispBinTrend.Rd man/dispCoxReid.Rd man/dispCoxReidInterpolateTagwise.Rd man/dispCoxReidSplineTrend.Rd man/dropEmptyLevels.Rd man/edgeR-package.Rd man/edgeRUsersGuide.Rd man/equalizeLibSizes.Rd man/estimateCommonDisp.Rd man/estimateDisp.Rd man/estimateExonGenewisedisp.Rd man/estimateGLMCommonDisp.Rd man/estimateGLMRobustDisp.Rd man/estimateGLMTagwiseDisp.Rd man/estimateGLMTrendedDisp.Rd man/estimateTagwiseDisp.Rd man/estimateTrendedDisp.Rd man/exactTest.Rd man/expandAsMatrix.Rd man/getCounts.Rd man/getPriorN.Rd man/gini.Rd man/glmQLFTest.Rd man/glmTreat.Rd man/glmfit.Rd man/goana.Rd man/gof.Rd man/goodTuring.Rd man/loessByCol.Rd man/maPlot.Rd man/makeCompressedMatrix.Rd man/maximizeInterpolant.Rd man/maximizeQuadratic.Rd man/meanvar.Rd man/mglm.Rd man/movingAverageByCol.Rd man/nbinomDeviance.Rd man/normalizeChIPtoInput.Rd man/plotBCV.Rd man/plotExonUsage.Rd man/plotMD.Rd man/plotMDS.DGEList.Rd man/plotQLDisp.Rd man/plotSmear.Rd man/plotSpliceDGE.Rd man/predFC.Rd man/processAmplicons.Rd man/q2qnbinom.Rd man/readDGE.Rd man/roast.DGEList.Rd man/romer.DGEList.Rd man/scaleOffset.Rd man/spliceVariants.Rd man/splitIntoGroups.Rd man/subsetting.Rd man/sumTechReps.Rd man/systematicSubset.Rd man/thinCounts.Rd man/topSpliceDGE.Rd man/topTags.Rd man/validDGEList.Rd man/weightedCondLogLikDerDelta.Rd man/zscoreNBinom.Rd
src
src/Makevars
src/R_add_prior_count.cpp
src/R_add_repeat_matrices.cpp
src/R_ave_log_cpm.cpp
src/R_calculate_cpm.cpp
src/R_check_counts.cpp
src/R_check_poisson_bound.cpp
src/R_compute_apl.cpp
src/R_compute_nbdev.cpp
src/R_exact_test_by_deviance.cpp
src/R_get_one_way_fitted.cpp
src/R_initialize_levenberg.cpp
src/R_levenberg.cpp
src/R_loess_by_col.cpp
src/R_maximize_interpolant.cpp
src/R_one_group.cpp
src/R_process_hairpin_reads.c
src/R_simple_good_turing.cpp
src/add_prior.cpp
src/add_prior.h
src/adj_coxreid.cpp
src/fmm_spline.c
src/glm.h
src/glm_levenberg.cpp
src/glm_one_group.cpp
src/init.cpp
src/interpolator.cpp
src/interpolator.h
src/matvec_check.cpp
src/matvec_check.h
src/nbdev.cpp
src/utils.h
tests
tests/edgeR-Tests.R
tests/edgeR-Tests.Rout.save
vignettes
vignettes/edgeR.Rnw

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