DGEExact-class          differential expression of Digital Gene
                        Expression data - class
DGEGLM-class            Digital Gene Expression Generalized Linear
                        Model results - class
DGELRT-class            Digital Gene Expression Likelihood Ratio Test
                        data and results - class
DGEList                 DGEList Constructor
DGEList-class           Digital Gene Expression data - class
WLEB                    Calculate Weighted Likelihood Empirical Bayes
                        Estimates
addPriorCount           Add a prior count
adjustedProfileLik      Adjusted Profile Likelihood for the Negative
                        Binomial Dispersion Parameter
as.data.frame.TopTags   Turn a TopTags Object into a Dataframe
as.matrix.DGEList       Turn a DGEList Object into a Matrix
aveLogCPM               Average Log Counts Per Million
binMeanVar              Explore the mean-variance relationship for DGE
                        data
binomTest               Exact Binomial Tests for Comparing Two Digital
                        Libraries
calcNormFactors         Calculate Normalization Factors to Align
                        Columns of a Count Matrix
camera.DGEList          Competitive Gene Set Test for Digital Gene
                        Expression Data Accounting for Inter-gene
                        Correlation
catchSalmon             Process Kallisto or Salmon Output
cbind                   Combine DGEList Objects
commonCondLogLikDerDelta
                        Conditional Log-Likelihoods in Terms of Delta
condLogLikDerSize       Conditional Log-Likelihood of the Dispersion
                        for a Single Group of Replicate Libraries
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
dglmStdResid            Visualize the mean-variance relationship in DGE
                        data using standardized residuals
diffSpliceDGE           Test for Differential Exon Usage
dim.DGEList             Retrieve the Dimensions of a DGEList, DGEExact,
                        DGEGLM, DGELRT or TopTags Object
dimnames.DGEList        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 Cox-Reid Adjusted Profile
                        Likelihood
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 Maximum Likelihood
estimateDisp            Estimate Common, Trended and Tagwise Negative
                        Binomial dispersions by weighted likelihood
                        empirical Bayes
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 Binomial GLMs using Observation
                        Weights
estimateGLMTagwiseDisp
                        Empirical Bayes Tagwise Dispersions for
                        Negative Binomial GLMs
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 Negative-Binomial Counts
expandAsMatrix          expandAsMatrix
filterByExpr            Filter Genes By Expression Level
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
glmQLFit                Genewise Negative Binomial Generalized Linear
                        Models with Quasi-likelihood Tests
glmTreat                Test for Differential Expression Relative to a
                        Threshold
goana.DGELRT            Gene Ontology or KEGG Analysis of
                        Differentially Expressed Genes
gof                     Goodness of Fit Tests for Multiple GLM Fits
goodTuring              Good-Turing Frequency Estimation
loessByCol              Locally Weighted Mean By Column
maPlot                  Plots Log-Fold Change versus Log-Concentration
                        (or, M versus A) for Count Data
makeCompressedMatrix    makeCompressedMatrix
maximizeInterpolant     Maximize a function given a table of values by
                        spline interpolation.
maximizeQuadratic       Maximize a function given a table of values by
                        quadratic interpolation.
mglm                    Fit Negative Binomial Generalized Linear Models
                        to Multiple Response Vectors: Low Level
                        Functions
modelMatrixMeth         Construct Design Matrix for edgeR Analysis of
                        Methylation Count Data
movingAverageByCol      Moving Average Smoother of Matrix Columns
nbinomDeviance          Negative Binomial Deviance
nbinomUnitDeviance      Negative Binomial Unit Deviance
nearestReftoX           Find Nearest Element of Reference for each
                        Element of X
nearestTSS              Find Nearest Transcriptional Start Site
normalizeChIPtoInput    Normalize ChIP-Seq Read Counts to Input and
                        Test for Enrichment
plotBCV                 Plot Biological Coefficient of Variation
plotExonUsage           Create a Plot of Exon Usage from Exon-Level
                        Count Data
plotMD.DGEList          Mean-Difference Plot of Count Data
plotMDS.DGEList         Multidimensional scaling plot of distances
                        between digital gene expression profiles
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 Distributions
read10X                 Read 10X Genomics Files
readBismark2DGE         Read Bismark Coverage Files
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
rowsum.DGEList          Sum Over Groups of Genes
scaleOffset             Scale offsets
spliceVariants          Identify Genes with Splice Variants
splitIntoGroups         Split the Counts or Pseudocounts from a DGEList
                        Object According To Group
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
                        Genes/Tags
validDGEList            Check for Valid DGEList object
weightedCondLogLikDerDelta
                        Weighted Conditional Log-Likelihood in Terms of
                        Delta
zscoreNBinom            Z-score Equivalents of Negative Binomial
                        Deviate
