edgeR-package	edgeR-package
adjustedProfileLik	adjustedProfileLik
as.data.frame.TopTags	asdataframe
as.matrix.DGEList	asmatrix
aveLogCPM	aveLogCPM
aveLogCPM.default	aveLogCPM
aveLogCPM.DGEGLM	aveLogCPM
aveLogCPM.DGEList	aveLogCPM
binMeanVar	meanvar
binomTest	binomTest
calcNormFactors	calcNormFactors
calcNormOffsetsforChIP	normalizeChIPtoInput
camera.DGEList	camera.DGEList
commonCondLogLikDerDelta	commonCondLogLikDerDelta
condLogLikDerDelta	condLogLikDerSize
condLogLikDerSize	condLogLikDerSize
cpm	cpm
cpm.default	cpm
cpm.DGEList	cpm
cutWithMinN	cutWithMinN
decideTestsDGE	decidetestsDGE
designAsFactor	mglm
DGEExact-class	DGEExact-class
DGEGLM-class	DGEGLM-class
DGEList	DGEList
DGEList-class	DGEList-class
DGELRT-class	DGELRT-class
dglmStdResid	dglmStdResid
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<-.DGEGLM	dimnames
dimnames<-.DGEList	dimnames
dispBinTrend	dispBinTrend
dispCoxReid	dispCoxReid
dispCoxReidInterpolateTagwise	dispCoxReidInterpolateTagwise
dispCoxReidPowerTrend	dispCoxReidSplineTrend
dispCoxReidSplineTrend	dispCoxReidSplineTrend
dispDeviance	dispCoxReid
dispPearson	dispCoxReid
edgeR	edgeR-package
edgeRUsersGuide	edgeRUsersGuide
equalizeLibSizes	equalizeLibSizes
estimateCommonDisp	estimateCommonDisp
estimateDisp	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
estimateTrendedDisp	estimateTrendedDisp
exactTest	exactTest
exactTestBetaApprox	exactTest
exactTestByDeviance	exactTest
exactTestBySmallP	exactTest
exactTestDoubleTail	exactTest
expandAsMatrix	expandAsMatrix
getCounts	getCounts
getDispersion	getCounts
getDispersions	dglmStdResid
getOffset	getCounts
getPriorN	getPriorN
glmFit	glmfit
glmFit.default	glmfit
glmFit.DGEList	glmfit
glmLRT	glmfit
glmQLFTest	glmfit
gof	gof
goodTuring	goodTuring
goodTuringPlot	goodTuring
goodTuringProportions	goodTuring
length.DGEExact	dim
length.DGEGLM	dim
length.DGEList	dim
length.DGELRT	dim
length.TopTags	dim
locfitByCol	loessByCol
loessByCol	loessByCol
maPlot	maPlot
maximizeInterpolant	maximizeInterpolant
maximizeQuadratic	maximizeQuadratic
mglm	mglm
mglmLevenberg	mglm
mglmOneGroup	mglm
mglmOneWay	mglm
movingAverageByCol	movingAverageByCol
mroast.DGEList	roast.DGEList
nbinomDeviance	nbinomDeviance
nbinomUnitDeviance	nbinomDeviance
normalizeChIPtoInput	normalizeChIPtoInput
plotBCV	plotBCV
plotExonUsage	plotExonUsage
plotMDS.DGEList	plotMDS.DGEList
plotMeanVar	meanvar
plotSmear	plotSmear
predFC	predFC
predFC.default	predFC
predFC.DGEList	predFC
processHairpinReads	processHairpinReads
q2qnbinom	q2qnbinom
q2qpois	q2qnbinom
readDGE	readDGE
roast.DGEList	roast.DGEList
rpkm	cpm
rpkm.default	cpm
rpkm.DGEList	cpm
show,DGEExact-method	DGEExact-class
show,DGEGLM-method	DGEGLM-class
show,DGELRT-method	DGELRT-class
show,TopTags-method	topTags
spliceVariants	spliceVariants
splitIntoGroups	splitIntoGroups
splitIntoGroupsPseudo	splitIntoGroups
subsetting	subsetting
sumTechReps	sumTechReps
sumTechReps.default	sumTechReps
sumTechReps.DGEList	sumTechReps
systematicSubset	systematicSubset
thinCounts	thinCounts
topTags	topTags
TopTags-class	topTags
validDGEList	validDGEList
weightedCondLogLikDerDelta	weightedCondLogLikDerDelta
WLEB	WLEB
zscoreNBinom	zscoreNBinom
[.DGEExact	subsetting
[.DGEGLM	subsetting
[.DGEList	subsetting
[.DGELRT	subsetting
[.TopTags	subsetting
