InPAS-package	InPAS-package
$,UTR3eSet-method	UTR3eSet
$<-,UTR3eSet-method	UTR3eSet
coverageFromBedGraph	coverageFromBedGraph
coverageRate	coverageRate
covThreshold	covThreshold
CPsites	CPsites
CPsite_estimation	CPsite_estimation
depthWeight	depthWeight
distalAdj	distalAdj
filterRes	filterRes
fisher.exact.test	fisher.exact.test
get.regions.coverage	get.regions.coverage
getCov	getCov
getUTR3eSet	getUTR3eSet
getUTR3region	getUTR3region
InPAS	InPAS-package
inPAS	inPAS
lastCDSusage	lastCDSusage
limmaAnalyze	limmaAnalyze
optimalSegmentation	optimalSegmentation
PAscore	PAscore
PAscore2	PAscore2
polishCPs	polishCPs
prepare4GSEA	prepare4GSEA
proximalAdj	proximalAdj
proximalAdjByCleanUpdTSeq	proximalAdjByCleanUpdTSeq
proximalAdjByPWM	proximalAdjByPWM
removeUTR3__UTR3	removeUTR3__UTR3
searchDistalCPs	searchDistalCPs
searchProximalCPs	searchProximalCPs
seqLen	seqLen
singleGroupAnalyze	singleGroupAnalyze
singleSampleAnalyze	singleSampleAnalyze
sortGR	sortGR
testUsage	testUsage
totalCoverage	totalCoverage
trimSeqnames	trimSeqnames
usage4plot	usage4plot
utr3.hg19	utr3.hg19
utr3.mm10	utr3.mm10
utr3Annotation	utr3Annotation
UTR3eSet	UTR3eSet
UTR3eSet-class	UTR3eSet
UTR3TotalCoverage	UTR3TotalCoverage
UTR3usage	UTR3usage
utr3UsageEstimation	utr3UsageEstimation
valley	valley
zScoreThrethold	zScoreThrethold
