addBroadTypes	addBroadTypes
addIntronInTranscript	addIntronInTranscript
addSets	addSets
alternativeIntronUsage	alternativeIntronUsage
annotateGeneModel	annotateGeneModel
attrChangeAltSpliced	attrChangeAltSpliced
coordinates	coordinates-methods
coordinates,whippetDataSet-method	coordinates-methods
cumsumANDpad	cumsumANDpad
DEXSeqIdsToGeneIds	DEXSeqIdsToGeneIds
diffSplicingResults	diffSplicingResults-methods
diffSplicingResults,whippetDataSet-method	diffSplicingResults-methods
exonsToTranscripts	exonsToTranscripts
filterGtfOverlap	filterGtfOverlap
filterWhippetEvents	filterWhippetEvents
findDEXexonType	findDEXexonType
findExonContainingTranscripts	findExonContainingTranscripts
findIntronContainingTranscripts	findIntronContainingTranscripts
findJunctionPairs	findJunctionPairs
formatWhippetEvents	formatWhippetEvents
getOrfs	getOrfs
getUOrfs	getUOrfs
junctions	junctions-methods
junctions,whippetDataSet-method	junctions-methods
leafcutterTranscriptChangeSummary	leafcutterTranscriptChangeSummary
makeGeneModel	makeGeneModel
maxLocation	maxLocation
orfDiff	orfDiff
orfSimilarity	orfSimilarity
overlapTypes	overlapTypes
readCounts	readCounts-methods
readCounts,whippetDataSet-method	readCounts-methods
readWhippetDataSet	readWhippetDataSet
readWhippetDIFFfiles	readWhippetDIFFfiles
readWhippetJNCfiles	readWhippetJNCfiles
readWhippetPSIfiles	readWhippetPSIfiles
removeDuplicateTranscripts	removeDuplicateTranscripts
removeSameExon	removeSameExon
removeVersion	removeVersion
reorderExonNumbers	reorderExonNumbers
replaceJunction	replaceJunction
skipExonInTranscript	skipExonInTranscript
summariseExonTypes	summariseExonTypes
transcriptChangeSummary	transcriptChangeSummary
UTR2UTR53	UTR2UTR53
whippetDataSet-class	whippetDataSet-class
whippetTranscriptChangeSummary	whippetTranscriptChangeSummary
