edgeR-package	edgeR-package
adjustedProfileLik	adjustedProfileLik
approx.expected.info	approx.expected.info
as.data.frame.TopTags	asdataframe
as.matrix.DGEList	asmatrix
betaApproxNBTest	betaApproxNBTest
binCMLDispersion	bin.dispersion
binGLMDispersion	bin.dispersion
binMeanVar	meanvar
binomTest	binomTest
calcNormFactors	calcNormFactors
calcNormOffsetsforChIP	normalizeChIPtoInput
commonCondLogLikDerDelta	commonCondLogLikDerDelta
condLogLikDerDelta	condLogLikDerDelta
condLogLikDerSize	condLogLikDerSize
cpm	cpm
cutWithMinN	cutWithMinN
decideTestsDGE	decidetestsDGE
designAsFactor	mglm
deviances.function	mglm
DGEExact-class	DGEExact-class
DGEGLM-class	DGEGLM
DGEList	DGEList
DGEList-class	DGEList-class
DGELRT-class	DGELRT
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.TopTags	dimnames
dimnames<-.DGEExact	dimnames
dimnames<-.DGEGLM	dimnames
dimnames<-.DGEList	dimnames
dimnames<-.TopTags	dimnames
dispBinTrend	dispBinTrend
dispCoxReid	dispCoxReid
dispCoxReidInterpolateTagwise	dispCoxReidInterpolateTagwise
dispCoxReidPowerTrend	dispCoxReidSplineTrend
dispCoxReidSplineTrend	dispCoxReidSplineTrend
dispDeviance	dispCoxReid
dispPearson	dispCoxReid
edgeR	edgeR-package
edgeRUsersGuide	edgeRUsersGuide
equalizeLibSizes	equalizeLibSizes
estimateCommonDisp	estimateCommonDisp
estimateExonGenewiseDisp	estimateExonGenewisedisp
estimateGLMCommonDisp	estimateGLMCommonDisp
estimateGLMCommonDisp.default	estimateGLMCommonDisp
estimateGLMCommonDisp.DGEList	estimateGLMCommonDisp
estimateGLMTagwiseDisp	estimateGLMTagwiseDisp
estimateGLMTagwiseDisp.default	estimateGLMTagwiseDisp
estimateGLMTagwiseDisp.DGEList	estimateGLMTagwiseDisp
estimateGLMTrendedDisp	estimateGLMTrendedDisp
estimateGLMTrendedDisp.default	estimateGLMTrendedDisp
estimateGLMTrendedDisp.DGEList	estimateGLMTrendedDisp
estimatePs	estimatePs
estimateSmoothing	estimateSmoothing
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
goodTuringProportions	goodTuring
length.DGEExact	dim
length.DGEGLM	dim
length.DGEList	dim
length.DGELRT	dim
length.TopTags	dim
logLikDerP	logLikDerP
maPlot	maPlot
maximizeInterpolant	maximizeInterpolant
maximizeQuadratic	maximizeQuadratic
mglm	mglm
mglmLevenberg	mglm
mglmLS	mglm
mglmOneGroup	mglm
mglmOneWay	mglm
mglmSimple	mglm
movingAverageByCol	movingAverageByCol
NC1	Tu102
NC2	Tu102
normalizeChIPtoInput	normalizeChIPtoInput
plotBCV	plotBCV
plotExonUsage	plotExonUsage
plotMDS.DGEList	plotMDS.dge
plotMeanVar	meanvar
plotSmear	plotSmear
predFC	predFC
predFC.default	predFC
predFC.DGEList	predFC
q2qnbinom	q2qnbinom
q2qpois	q2qnbinom
readDGE	readDGE
show,DGEExact-method	DGEExact-class
show,DGEGLM-method	DGEGLM
show,DGELRT-method	DGELRT
show,TopTags-method	topTags
spliceVariants	spliceVariants
splitIntoGroups	splitIntoGroups
splitIntoGroupsPseudo	splitIntoGroups
subsetting	subsetting
systematicSubset	systematicSubset
thinCounts	thinCounts
topTags	topTags
TopTags-class	topTags
Tu102	Tu102
Tu98	Tu102
weightedComLik	weightedComLik
weightedComLikMA	weightedComLik
weightedCondLogLikDerDelta	weightedCondLogLikDerDelta
zscoreNBinom	zscoreNBinom
[.DGEExact	subsetting
[.DGEGLM	subsetting
[.DGEList	subsetting
[.DGELRT	subsetting
[.TopTags	topTags
