edgeR-package	edgeR-package
addPriorCount	addPriorCount
adjustedProfileLik	adjustedProfileLik
as.data.frame.DGEExact	asdataframe
as.data.frame.DGEGLM	asdataframe
as.data.frame.DGEList	asdataframe
as.data.frame.DGELRT	asdataframe
as.data.frame.TopTags	asdataframe
as.matrix.CompressedMatrix	makeCompressedMatrix
as.matrix.DGEGLM	asmatrix
as.matrix.DGEList	asmatrix
aveLogCPM	aveLogCPM
aveLogCPM.default	aveLogCPM
aveLogCPM.DGEGLM	aveLogCPM
aveLogCPM.DGEList	aveLogCPM
aveLogCPM.SummarizedExperiment	aveLogCPM
binMeanVar	meanvar
binomTest	binomTest
calcNormFactors	calcNormFactors
calcNormFactors.default	calcNormFactors
calcNormFactors.DGEList	calcNormFactors
calcNormFactors.SummarizedExperiment	calcNormFactors
calcNormOffsetsforChIP	normalizeChIPtoInput
camera.DGEGLM	camera
camera.DGEList	camera
cameraPR.DGELRT	camera
catchKallisto	catchSalmon
catchRSEM	catchSalmon
catchSalmon	catchSalmon
cbind	cbind
cbind.CompressedMatrix	makeCompressedMatrix
cbind.DGEList	cbind
commonCondLogLikDerDelta	commonCondLogLikDerDelta
CompressedMatrix	makeCompressedMatrix
CompressedMatrix-class	makeCompressedMatrix
condLogLikDerDelta	condLogLikDerSize
condLogLikDerSize	condLogLikDerSize
cpm	cpm
cpm.default	cpm
cpm.DGEGLM	cpm
cpm.DGEList	cpm
cpm.DGELRT	cpm
cpm.SummarizedExperiment	cpm
cpmByGroup	cpm
cpmByGroup.default	cpm
cpmByGroup.DGEList	cpm
cpmByGroup.SummarizedExperiment	cpm
cutWithMinN	cutWithMinN
decideTests.DGEExact	decidetestsDGE
decideTests.DGELRT	decidetestsDGE
designAsFactor	mglm
DGEExact-class	DGEExact-class
DGEGLM-class	DGEGLM-class
DGEList	DGEList
DGEList-class	DGEList-class
DGEList.data.frame	DGEList
DGEList.default	DGEList
DGELRT-class	DGELRT-class
diffSplice.DGEGLM	diffSplice
diffSpliceDGE	diffSpliceDGE
dim.CompressedMatrix	makeCompressedMatrix
dim.DGEExact	dim
dim.DGEGLM	dim
dim.DGEList	dim
dim.DGELRT	dim
dim.TopTags	dim
dimnames.DGEExact	dimnames
dimnames.DGEGLM	dimnames
dimnames.DGEList	dimnames
dimnames.DGELRT	dimnames
dimnames.TopTags	dimnames
dimnames<-.DGEExact	dimnames
dimnames<-.DGEGLM	dimnames
dimnames<-.DGEList	dimnames
dimnames<-.DGELRT	dimnames
dispBinTrend	dispBinTrend
dispCoxReid	dispCoxReid
dispCoxReidInterpolateTagwise	dispCoxReidInterpolateTagwise
dispCoxReidPowerTrend	dispCoxReidSplineTrend
dispCoxReidSplineTrend	dispCoxReidSplineTrend
dispDeviance	dispCoxReid
dispPearson	dispCoxReid
dropEmptyLevels	dropEmptyLevels
edgeR	edgeR-package
edgeRUsersGuide	edgeRUsersGuide
equalizeLibSizes	equalizeLibSizes
equalizeLibSizes.default	equalizeLibSizes
equalizeLibSizes.DGEList	equalizeLibSizes
estimateCommonDisp	estimateCommonDisp
estimateCommonDisp.default	estimateCommonDisp
estimateCommonDisp.DGEList	estimateCommonDisp
estimateDisp	estimateDisp
estimateDisp.default	estimateDisp
estimateDisp.DGEList	estimateDisp
estimateDisp.SummarizedExperiment	estimateDisp
estimateExonGenewiseDisp	estimateExonGenewisedisp
estimateGLMCommonDisp	estimateGLMCommonDisp
estimateGLMCommonDisp.default	estimateGLMCommonDisp
estimateGLMCommonDisp.DGEList	estimateGLMCommonDisp
estimateGLMRobustDisp	estimateGLMRobustDisp
estimateGLMTagwiseDisp	estimateGLMTagwiseDisp
estimateGLMTagwiseDisp.default	estimateGLMTagwiseDisp
estimateGLMTagwiseDisp.DGEList	estimateGLMTagwiseDisp
estimateGLMTrendedDisp	estimateGLMTrendedDisp
estimateGLMTrendedDisp.default	estimateGLMTrendedDisp
estimateGLMTrendedDisp.DGEList	estimateGLMTrendedDisp
estimateTagwiseDisp	estimateTagwiseDisp
estimateTagwiseDisp.default	estimateTagwiseDisp
estimateTagwiseDisp.DGEList	estimateTagwiseDisp
estimateTrendedDisp	estimateTrendedDisp
estimateTrendedDisp.default	estimateTrendedDisp
estimateTrendedDisp.DGEList	estimateTrendedDisp
exactTest	exactTest
exactTestBetaApprox	exactTest
exactTestByDeviance	exactTest
exactTestBySmallP	exactTest
exactTestDoubleTail	exactTest
expandAsMatrix	expandAsMatrix
featureCounts2DGEList	featureCounts2DGEList
filterByExpr	filterByExpr
filterByExpr.default	filterByExpr
filterByExpr.DGEList	filterByExpr
filterByExpr.SummarizedExperiment	filterByExpr
fry.DGEGLM	roast.DGEGLM
fry.DGEList	roast.DGEList
getCounts	getCounts
getDispersion	getCounts
getNormLibSizes	effectiveLibSizes
getNormLibSizes.default	effectiveLibSizes
getNormLibSizes.DGEGLM	effectiveLibSizes
getNormLibSizes.DGEList	effectiveLibSizes
getNormLibSizes.DGELRT	effectiveLibSizes
getOffset	getCounts
getPriorN	getPriorN
gini	gini
glmFit	glmfit
glmFit.default	glmfit
glmFit.DGEList	glmfit
glmFit.SummarizedExperiment	glmfit
glmLRT	glmLRT
glmQLFit	glmQLFit
glmQLFit.default	glmQLFit
glmQLFit.DGEList	glmQLFit
glmQLFit.SummarizedExperiment	glmQLFit
glmQLFTest	glmQLFTest
glmTreat	glmTreat
goana.DGEExact	goana
goana.DGELRT	goana
gof	gof
goodTuring	goodTuring
goodTuringPlot	goodTuring
goodTuringProportions	goodTuring
head.DGEExact	head
head.DGEGLM	head
head.DGEList	head
head.DGELRT	head
head.TopTags	head
kegga.DGEExact	goana
kegga.DGELRT	goana
length.CompressedMatrix	makeCompressedMatrix
locfitByCol	loessByCol
loessByCol	loessByCol
makeCompressedMatrix	makeCompressedMatrix
maPlot	maPlot
maximizeInterpolant	maximizeInterpolant
maximizeQuadratic	maximizeQuadratic
mglm	mglm
mglmLevenberg	mglm
mglmOneGroup	mglm
mglmOneWay	mglm
modelMatrixMeth	modelMatrixMeth
movingAverageByCol	movingAverageByCol
mroast.DGEGLM	roast.DGEGLM
mroast.DGEList	roast.DGEList
nbinomDeviance	nbinomDeviance
nbinomUnitDeviance	nbinomUnitDeviance
nearestReftoX	nearestReftoX
nearestTSS	nearestTSS
normalizeBetweenArrays.DGEList	normalizeBetweenArraysDGEList
normalizeChIPtoInput	normalizeChIPtoInput
normLibSizes	calcNormFactors
normLibSizes.default	calcNormFactors
normLibSizes.DGEList	calcNormFactors
normLibSizes.SummarizedExperiment	calcNormFactors
Ops.CompressedMatrix	makeCompressedMatrix
plotBCV	plotBCV
plotExonUsage	plotExonUsage
plotMD.DGEExact	plotMD
plotMD.DGEGLM	plotMD
plotMD.DGEList	plotMD
plotMD.DGELRT	plotMD
plotMD.SummarizedExperiment	plotMD
plotMDS.DGEList	plotMDS.DGEList
plotMDS.SummarizedExperiment	plotMDS.DGEList
plotMeanVar	meanvar
plotMeanVar2	dglmStdResid
plotQLDisp	plotQLDisp
plotSmear	plotSmear
plotSpliceDGE	plotSpliceDGE
predFC	predFC
predFC.default	predFC
predFC.DGEList	predFC
predFC.SummarizedExperiment	predFC
processAmplicons	processAmplicons
q2qnbinom	q2qnbinom
q2qpois	q2qnbinom
rbind.CompressedMatrix	makeCompressedMatrix
rbind.DGEList	cbind
read10X	read10X
readBismark2DGE	readBismark2DGE
readDGE	readDGE
roast.DGEGLM	roast.DGEGLM
roast.DGEList	roast.DGEList
romer.DGEGLM	romer.DGEGLM
romer.DGEList	romer.DGEList
rowsum.DGEList	rowsum
rowsum.SummarizedExperiment	rowsum
rpkm	cpm
rpkm.default	cpm
rpkm.DGEGLM	cpm
rpkm.DGEList	cpm
rpkm.DGELRT	cpm
rpkm.SummarizedExperiment	cpm
rpkmByGroup	cpm
rpkmByGroup.default	cpm
rpkmByGroup.DGEList	cpm
rpkmByGroup.SummarizedExperiment	cpm
scaleOffset	scaleOffset
scaleOffset.default	scaleOffset
scaleOffset.DGEList	scaleOffset
SE2DGEList	SE2DGEList
Seurat2PB	Seurat2PB
show,DGEExact-method	DGEExact-class
show,DGEGLM-method	DGEGLM-class
show,DGELRT-method	DGELRT-class
show,TopTags-method	topTags
spliceVariants	spliceVariants
splitIntoGroups	splitIntoGroups
splitIntoGroups.default	splitIntoGroups
splitIntoGroups.DGEList	splitIntoGroups
splitIntoGroupsPseudo	splitIntoGroups
subsetting	subsetting
sumTechReps	sumTechReps
sumTechReps.default	sumTechReps
sumTechReps.DGEList	sumTechReps
sumTechReps.SummarizedExperiment	sumTechReps
systematicSubset	systematicSubset
tail.DGEExact	head
tail.DGEGLM	head
tail.DGEList	head
tail.DGELRT	head
tail.TopTags	head
thinCounts	thinCounts
topSpliceDGE	topSpliceDGE
topTags	topTags
TopTags-class	topTags
validDGEList	validDGEList
voomLmFit	voomLmFit
weightedCondLogLikDerDelta	weightedCondLogLikDerDelta
WLEB	WLEB
zscoreNBinom	zscoreNBinom
[.CompressedMatrix	makeCompressedMatrix
[.DGEExact	subsetting
[.DGEGLM	subsetting
[.DGEList	subsetting
[.DGELRT	subsetting
[.TopTags	subsetting
[<-.CompressedMatrix	makeCompressedMatrix
