ORFik-package	ORFik-package
addCdsOnLeaderEnds	addCdsOnLeaderEnds
addNewTSSOnLeaders	addNewTSSOnLeaders
allFeaturesHelper	allFeaturesHelper
assignAnnotations	assignAnnotations
assignFirstExonsStartSite	assignFirstExonsStartSite
assignLastExonsStopSite	assignLastExonsStopSite
assignTSSByCage	assignTSSByCage
asTX	asTX
bamVarName	bamVarName
bamVarNamePicker	bamVarNamePicker
bedToGR	bedToGR
changePointAnalysis	changePointAnalysis
checkRFP	checkRFP
checkRNA	checkRNA
codonSumsPerGroup	codonSumsPerGroup
computeFeatures	computeFeatures
computeFeaturesCage	computeFeaturesCage
convertToOneBasedRanges	convertToOneBasedRanges
coverageGroupings	coverageGroupings
coverageHeatMap	coverageHeatMap
coveragePerTiling	coveragePerTiling
coverageScorings	coverageScorings
create.experiment	create.experiment
defineIsoform	defineIsoform
defineTrailer	defineTrailer
detectRibosomeShifts	detectRibosomeShifts
disengagementScore	disengagementScore
distToCds	distToCds
distToTSS	distToTSS
downstreamFromPerGroup	downstreamFromPerGroup
downstreamN	downstreamN
downstreamOfPerGroup	downstreamOfPerGroup
entropy	entropy
experiment	experiment-class
experiment-class	experiment-class
extendLeaders	extendLeaders
extendsTSSexons	extendsTSSexons
extendTrailers	extendTrailers
filterCage	filterCage
filterTranscripts	filterTranscripts
filterUORFs	filterUORFs
fimport	fimport
findFa	findFa
findFromPath	findFromPath
findLibrariesInFolder	findLibrariesInFolder
findMapORFs	findMapORFs
findMaxPeaks	findMaxPeaks
findNewTSS	findNewTSS
findORFs	findORFs
findORFsFasta	findORFsFasta
findUORFs	findUORFs
firstEndPerGroup	firstEndPerGroup
firstExonPerGroup	firstExonPerGroup
firstStartPerGroup	firstStartPerGroup
floss	floss
fpkm	fpkm
fpkm_calc	fpkm_calc
fractionLength	fractionLength
fread.bed	fread.bed
gcContent	gcContent
getNGenesCoverage	getNGenesCoverage
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
kozakHeatmap	kozakHeatmap
kozakSequenceScore	kozakSequenceScore
lastExonEndPerGroup	lastExonEndPerGroup
lastExonPerGroup	lastExonPerGroup
lastExonStartPerGroup	lastExonStartPerGroup
libraryTypes	libraryTypes
loadRegion	loadRegion
loadRegions	loadRegions
loadTranscriptType	loadTranscriptType
loadTxdb	loadTxdb
longestORFs	longestORFs
makeExonRanks	makeExonRanks
makeORFNames	makeORFNames
mapToGRanges	mapToGRanges
matchColors	matchColors
matchNaming	matchNaming
matchSeqStyle	matchSeqStyle
metaWindow	metaWindow
nrow,experiment-method	nrow-experiment-method
numCodons	numCodons
numExonsPerGroup	numExonsPerGroup
optimizeReads	optimizeReads
orfID	orfID
ORFik	ORFik-package
orfScore	orfScore
outputLibs	outputLibs
overlapsToCoverage	overlapsToCoverage
parseCigar	parseCigar
pmapFromTranscriptF	pmapFromTranscriptF
prettyScoring	prettyScoring
pSitePlot	pSitePlot
rankOrder	rankOrder
read.experiment	read.experiment
readBam	readBam
readWidths	readWidths
readWig	readWig
reassignTSSbyCage	reassignTSSbyCage
reassignTxDbByCage	reassignTxDbByCage
reduceKeepAttr	reduceKeepAttr
remakeTxdbExonIds	remakeTxdbExonIds
removeMetaCols	removeMetaCols
removeORFsWithinCDS	removeORFsWithinCDS
removeORFsWithSameStartAsCDS	removeORFsWithSameStartAsCDS
removeORFsWithSameStopAsCDS	removeORFsWithSameStopAsCDS
removeORFsWithStartInsideCDS	removeORFsWithStartInsideCDS
removeTxdbExons	removeTxdbExons
removeTxdbTranscripts	removeTxdbTranscripts
restrictTSSByUpstreamLeader	restrictTSSByUpstreamLeader
ribosomeReleaseScore	ribosomeReleaseScore
ribosomeStallingScore	ribosomeStallingScore
save.experiment	save.experiment
savePlot	savePlot
scaledWindowPositions	scaledWindowPositions
seqnamesPerGroup	seqnamesPerGroup
shiftFootprints	shiftFootprints
show,experiment-method	show-experiment-method
sortPerGroup	sortPerGroup
splitIn3Tx	splitIn3Tx
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
txNamesToGeneNames	txNamesToGeneNames
txSeqsFromFa	txSeqsFromFa
uniqueGroups	uniqueGroups
uniqueOrder	uniqueOrder
unlistGrl	unlistGrl
uORFSearchSpace	uORFSearchSpace
updateTxdbRanks	updateTxdbRanks
updateTxdbStartSites	updateTxdbStartSites
upstreamFromPerGroup	upstreamFromPerGroup
upstreamOfPerGroup	upstreamOfPerGroup
validateExperiments	validateExperiments
validGRL	validGRL
validSeqlevels	validSeqlevels
widthPerGroup	widthPerGroup
windowCoveragePlot	windowCoveragePlot
windowPerGroup	windowPerGroup
windowPerReadLength	windowPerReadLength
windowPerTranscript	windowPerTranscript
xAxisScaler	xAxisScaler
yAxisScaler	yAxisScaler
