chimera-package	chimera-package
addGA	class.fSet
addGA,fSet-method	class.fSet
addRNA	class.fSet
addRNA,fSet-method	class.fSet
bam2fastq	bam2fastq
breakpointOverlaps	breakpointOverlaps
chimera	chimera-package
chimeraSeqs	chimeraSeqs
chimeraSeqSet	chimeraSeqSet
defuseTPTN	defuseTPTN
filterList	filterList
filterSamReads	filterSamReads
fSet	class.fSet
fSet-class	class.fSet
fusionData	class.fSet
fusionData,fSet-method	class.fSet
fusionGA	class.fSet
fusionGA,fSet-method	class.fSet
fusionGRL	class.fSet
fusionGRL,fSet-method	class.fSet
fusionName	fusionName
fusionPeptides	fusionPeptides
fusionRNA	class.fSet
fusionRNA,fSet-method	class.fSet
gapfillerInstallation	gapfillerInstallation
gapfillerRun	gapfillerRun
gapfillerWrap	gapfillerWrap
importFusionData	importFusionData
is.fSet	is.fSet
MHmakeRandomString	MHmakeRandomString
newfSet	newfSet
newfSet,fSet-method	class.fSet
oncofuseInstallation	oncofuseInstallation
oncofuseRun	oncofuseRun
picardInstallation	picardInstallation
plotCoverage	plotCoverage
prettyPrint	prettyPrint
removingErrorLine	removingErrorLine
starInstallation	starInstallation
starReads	starReads
starRun	starRun
subreadRun	subreadRun
supportingReads	supportingReads
tophatInstallation	tophatInstallation
tophatRun	tophatRun
validateSamFile	validateSamFile
