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.

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>
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

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/scaleOffset.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/scaleOffset.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

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