dropEmptyLevels

Drop Levels of a Factor that Never Occur

WLEB

Calculate Weighted Likelihood Empirical Bayes Estimates

estimateGLMTagwiseDisp

Empirical Bayes Tagwise Dispersions for Negative Binomial GLMs

gini

Gini dispersion index

gof

Goodness of Fit Tests for Multiple GLM Fits

dispCoxReidSplineTrend

Estimate Dispersion Trend for Negative Binomial GLMs

nbinomDeviance

Negative Binomial Deviance

DGELRT-class

Digital Gene Expression Likelihood Ratio Test data and results - class

DGEExact-class

differential expression of Digital Gene Expression data - class

calcNormFactors

Calculate Normalization Factors to Align Columns of a Count Matrix

predFC

Predictive log-fold changes

edgeR-package

Empirical analysis of digital gene expression data in R

aveLogCPM

Average Log Counts Per Million

decideTestsDGE

Multiple Testing Across Genes and Contrasts

loessByCol

Locally Weighted Mean By Column

plotExonUsage

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

dim

Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object

plotSpliceDGE

Differential splicing plot

processAmplicons

Process raw data from pooled genetic sequencing screens

dispCoxReidInterpolateTagwise

Estimate Genewise Dispersion for Negative Binomial GLMs by Cox-Reid Adjusted Profile Likelihood

binomTest

Exact Binomial Tests for Comparing Two Digital Libraries

movingAverageByCol

Moving Average Smoother of Matrix Columns

expandAsMatrix

expandAsMatrix

splitIntoGroups

Split the Counts or Pseudocounts from a DGEList Object According To Group

estimateGLMCommonDisp

Estimate Common Dispersion for Negative Binomial GLMs

weightedCondLogLikDerDelta

Weighted Conditional Log-Likelihood in Terms of Delta

topSpliceDGE

Top table of differentially spliced genes or exons

estimateTagwiseDisp

Estimate Empirical Bayes Tagwise Dispersion Values

plotMDS.DGEList

Multidimensional scaling plot of distances between digital gene expression profiles

diffSpliceDGE

Test for Differential Exon Usage

meanvar

Explore the mean-variance relationship for DGE data

glmFit

Genewise Negative Binomial Generalized Linear Models

goodTuring

Good-Turing Frequency Estimation

normalizeChIPtoInput

Normalize ChIP-Seq Read Counts to Input and Test for Enrichment

plotSmear

Plots log-Fold Change versus log-Concentration (or, M versus A) for Count Data

plotMD.DGEList

Mean-Difference Plot of Count Data

zscoreNBinom

Z-score Equivalents of Negative Binomial Deviate

topTags

Table of the Top Differentially Expressed Tags

dispCoxReid

Estimate Common Dispersion for Negative Binomial GLMs

goana.DGELRT

Gene Ontology or KEGG Analysis of Differentially Expressed Genes

estimateExonGenewiseDisp

Estimate Genewise Dispersions from Exon-Level Count Data

estimateGLMTrendedDisp

Estimate Trended Dispersion for Negative Binomial GLMs

estimateGLMRobustDisp

Empirical Robust Bayes Tagwise Dispersions for Negative Binomial GLMs using Observation Weights

estimateTrendedDisp

Estimate Empirical Bayes Trended Dispersion Values

maximizeQuadratic

Maximize a function given a table of values by quadratic interpolation.

DGEGLM-class

Digital Gene Expression Generalized Linear Model results - class

commonCondLogLikDerDelta

Conditional Log-Likelihoods in Terms of Delta

sumTechReps

Sum Over Replicate Samples

subsetting

Subset DGEList, DGEGLM, DGEExact and DGELRT Objects

spliceVariants

Identify Genes with Splice Variants

thinCounts

Binomial or Multinomial Thinning of Counts

glmQLFit

Genewise Negative Binomial Generalized Linear Models with Quasi-likelihood Tests

equalizeLibSizes

Equalize Library Sizes by Quantile-to-Quantile Normalization

dglmStdResid

Visualize the mean-variance relationship in DGE data using standardized residuals

DGEList-class

Digital Gene Expression data - class

condLogLikDerSize

Conditional Log-Likelihood of the Dispersion for a Single Group of Replicate Libraries

estimateDisp

Estimate Common, Trended and Tagwise Negative Binomial dispersions by weighted likelihood empirical Bayes

adjustedProfileLik

Adjusted Profile Likelihood for the Negative Binomial Dispersion Parameter

cpm

Counts per Million or Reads per Kilobase per Million

estimateCommonDisp

Estimate Common Negative Binomial Dispersion by Conditional Maximum Likelihood

cutWithMinN

Cut numeric vector into non-empty intervals

as.data.frame

Turn a TopTags Object into a Dataframe

as.matrix

Turn a DGEList Object into a Matrix

DGEList

DGEList Constructor

camera.DGEList

Competitive Gene Set Test for Digital Gene Expression Data Accounting for Inter-gene Correlation

getCounts

Extract Specified Component of a DGEList Object

dimnames

Retrieve the Dimension Names of a DGE Object

getPriorN

Get a Recommended Value for Prior N from DGEList Object

glmTreat

Test for Differential Expression Relative to a Threshold

mglm

Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors: Low Level Functions

validDGEList

Check for Valid DGEList object

exactTest

Exact Tests for Differences between Two Groups of Negative-Binomial Counts

maximizeInterpolant

Maximize a function given a table of values by spline interpolation.

systematicSubset

Take a systematic subset of indices.

q2qnbinom

Quantile to Quantile Mapping between Negative-Binomial Distributions

readDGE

Read and Merge a Set of Files Containing Count Data

maPlot

Plots Log-Fold Change versus Log-Concentration (or, M versus A) for Count Data

plotBCV

Plot Biological Coefficient of Variation

roast.DGEList

Rotation Gene Set Tests for Digital Gene Expression Data

romer.DGEList

Rotation Gene Set Tests for Digital Gene Expression Data

plotQLDisp

Plot the quasi-likelihood dispersion

dispBinTrend

Estimate Dispersion Trend by Binning for NB GLMs

edgeRUsersGuide

View edgeR User's Guide