edgeR: Empirical Analysis of Digital Gene Expression Data in R

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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.

Author
Yunshun 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>
Date of publication
None
Maintainer
Yunshun 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>
License
GPL (>=2)
Version
3.16.4
URLs

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
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

Files in this package

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