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.danRer10	utr3.danRer10
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
