chimera-package	chimera-package
addGA	class.fSet
addGA,fSet-method	class.fSet
addRNA	class.fSet
addRNA,fSet-method	class.fSet
bam2fastq	bam2fastq
chimera	chimera-package
chimeraSeqs	chimeraSeqs
chimeraSeqSet	chimeraSeqSet
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
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
