ORFik-package	ORFik-package
addCdsOnLeaderEnds	addCdsOnLeaderEnds
addNewTSSOnLeaders	addNewTSSOnLeaders
allFeaturesHelper	allFeaturesHelper
assignAnnotations	assignAnnotations
assignFirstExonsStartSite	assignFirstExonsStartSite
assignLastExonsStopSite	assignLastExonsStopSite
assignTSSByCage	assignTSSByCage
asTX	asTX
bedToGR	bedToGR
changePointAnalysis	changePointAnalysis
checkRFP	checkRFP
checkRNA	checkRNA
codonSumsPerGroup	codonSumsPerGroup
computeFeatures	computeFeatures
computeFeaturesCage	computeFeaturesCage
convertToOneBasedRanges	convertToOneBasedRanges
coverageGroupings	coverageGroupings
coverageHeatMap	coverageHeatMap
coveragePerTiling	coveragePerTiling
coverageScorings	coverageScorings
defineIsoform	defineIsoform
defineTrailer	defineTrailer
detectRibosomeShifts	detectRibosomeShifts
disengagementScore	disengagementScore
distToCds	distToCds
distToTSS	distToTSS
downstreamFromPerGroup	downstreamFromPerGroup
downstreamN	downstreamN
downstreamOfPerGroup	downstreamOfPerGroup
entropy	entropy
extendLeaders	extendLeaders
extendsTSSexons	extendsTSSexons
filterCage	filterCage
filterTranscripts	filterTranscripts
findFa	findFa
findMapORFs	findMapORFs
findMaxPeaks	findMaxPeaks
findNewTSS	findNewTSS
findORFs	findORFs
findORFsFasta	findORFsFasta
firstEndPerGroup	firstEndPerGroup
firstExonPerGroup	firstExonPerGroup
firstStartPerGroup	firstStartPerGroup
floss	floss
fpkm	fpkm
fpkm_calc	fpkm_calc
fractionLength	fractionLength
fread.bed	fread.bed
gcContent	gcContent
groupGRangesBy	groupGRangesBy
groupings	groupings
gSort	gSort
hasHits	hasHits
initiationScore	initiationScore
insideOutsideORF	insideOutsideORF
is.grl	is.grl
is.gr_or_grl	is.gr_or_grl
is.ORF	is.ORF
isInFrame	isInFrame
isOverlapping	isOverlapping
isPeriodic	isPeriodic
kozakSequenceScore	kozakSequenceScore
lastExonEndPerGroup	lastExonEndPerGroup
lastExonPerGroup	lastExonPerGroup
lastExonStartPerGroup	lastExonStartPerGroup
loadRegion	loadRegion
loadTxdb	loadTxdb
longestORFs	longestORFs
makeExonRanks	makeExonRanks
makeORFNames	makeORFNames
mapToGRanges	mapToGRanges
matchNaming	matchNaming
metaWindow	metaWindow
numCodons	numCodons
numExonsPerGroup	numExonsPerGroup
optimizeReads	optimizeReads
orfID	orfID
ORFik	ORFik-package
orfScore	orfScore
overlapsToCoverage	overlapsToCoverage
parseCigar	parseCigar
pmapFromTranscriptF	pmapFromTranscriptF
pSitePlot	pSitePlot
rankOrder	rankOrder
readWidths	readWidths
reassignTSSbyCage	reassignTSSbyCage
reassignTxDbByCage	reassignTxDbByCage
reduceKeepAttr	reduceKeepAttr
remakeTxdbExonIds	remakeTxdbExonIds
removeMetaCols	removeMetaCols
removeTxdbExons	removeTxdbExons
removeTxdbTranscripts	removeTxdbTranscripts
restrictTSSByUpstreamLeader	restrictTSSByUpstreamLeader
ribosomeReleaseScore	ribosomeReleaseScore
ribosomeStallingScore	ribosomeStallingScore
savePlot	savePlot
scaledWindowPositions	scaledWindowPositions
seqnamesPerGroup	seqnamesPerGroup
shiftFootprints	shiftFootprints
sortPerGroup	sortPerGroup
startCodons	startCodons
startDefinition	startDefinition
startRegion	startRegion
startRegionCoverage	startRegionCoverage
startRegionString	startRegionString
startSites	startSites
stopCodons	stopCodons
stopDefinition	stopDefinition
stopSites	stopSites
strandBool	strandBool
strandPerGroup	strandPerGroup
subsetCoverage	subsetCoverage
subsetToFrame	subsetToFrame
tile1	tile1
translationalEff	translationalEff
txNames	txNames
txSeqsFromFa	txSeqsFromFa
uniqueGroups	uniqueGroups
uniqueOrder	uniqueOrder
unlistGrl	unlistGrl
uORFSearchSpace	uORFSearchSpace
updateTxdbRanks	updateTxdbRanks
updateTxdbStartSites	updateTxdbStartSites
upstreamFromPerGroup	upstreamFromPerGroup
upstreamOfPerGroup	upstreamOfPerGroup
validGRL	validGRL
validSeqlevels	validSeqlevels
widthPerGroup	widthPerGroup
windowCoveragePlot	windowCoveragePlot
windowPerGroup	windowPerGroup
windowPerReadLength	windowPerReadLength
windowPerTranscript	windowPerTranscript
