AddAndCheckDBSClassInVCF	AddAndCheckDBSClassInVCF
AddAndCheckSBSClassInVCF	AddAndCheckSBSClassInVCF
AddDBSClass	AddDBSClass
AddRunInformation	AddRunInformation
AddSBSClass	AddSBSClass
AddSeqContext	AddSeqContext
AddTranscript	AddTranscript
all.abundance	all.abundance
AnnotateDBSVCF	AnnotateDBSVCF
AnnotateIDVCF	AnnotateIDVCF
AnnotateSBSVCF	AnnotateSBSVCF
as.catalog	as.catalog
CalBaseCountsFrom3MerAbundance	CalBaseCountsFrom3MerAbundance
CalculateNumberOfSpace	CalculateNumberOfSpace
Canonicalize1Del	Canonicalize1Del
Canonicalize1ID	Canonicalize1ID
Canonicalize1INS	Canonicalize1INS
CanonicalizeID	CanonicalizeID
catalog.row.order	CatalogRowOrder
CatalogRowOrder	CatalogRowOrder
CheckAndFixChrNames	CheckAndFixChrNames
CheckAndFixChrNamesForTransRanges	CheckAndFixChrNamesForTransRanges
CheckAndReorderRownames	CheckAndReorderRownames
CheckAndReturnDBSCatalogs	CheckAndReturnDBSCatalogs
CheckAndReturnDBSMatrix	CheckAndReturnDBSMatrix
CheckAndReturnIDCatalog	CheckAndReturnIDCatalog
CheckAndReturnIDMatrix	CheckAndReturnIDMatrix
CheckAndReturnSBSCatalogs	CheckAndReturnSBSCatalogs
CheckAndReturnSBSMatrix	CheckAndReturnSBSMatrix
CheckDBSClassInVCF	CheckDBSClassInVCF
CheckSBSClassInVCF	CheckSBSClassInVCF
CheckSeqContextInVCF	CheckSeqContextInVCF
Collapse144CatalogTo78	CollapseCatalog
Collapse1536CatalogTo96	CollapseCatalog
Collapse192CatalogTo96	CollapseCatalog
CollapseCatalog	CollapseCatalog
ConvertICAMSCatalogToSigProSBS96	ConvertICAMSCatalogToSigProSBS96
CreateDinucAbundance	CreateDinucAbundance
CreateExomeStrandedRanges	CreateExomeStrandedRanges
CreateOneColDBSMatrix	CreateOneColDBSMatrix
CreateOneColIDMatrix	CreateOneColIDMatrix
CreateOneColSBSMatrix	CreateOneColSBSMatrix
CreateOnePPMFromSBSVCF	CreateOnePPMFromSBSVCF
CreatePentanucAbundance	CreatePentanucAbundance
CreatePPMFromSBSVCFs	CreatePPMFromSBSVCFs
CreateStrandedDinucAbundance	CreateStrandedDinucAbundance
CreateStrandedTrinucAbundance	CreateStrandedTrinucAbundance
CreateTetranucAbundance	CreateTetranucAbundance
CreateTransRanges	CreateTransRanges
CreateTrinucAbundance	CreateTrinucAbundance
FindDelMH	FindDelMH
FindMaxRepeatDel	FindMaxRepeatDel
FindMaxRepeatIns	FindMaxRepeatIns
gene.expression.data.HepG2	GeneExpressionData
gene.expression.data.MCF10A	GeneExpressionData
GeneExpressionData	GeneExpressionData
GenerateEmptyKmerCounts	GenerateEmptyKmerCounts
GenerateKmer	GenerateKmer
GetConsensusVAF	GetConsensusVAF
GetCustomKmerCounts	GetCustomKmerCounts
GetFreebayesVAF	GetVAF
GetGenomeKmerCounts	GetGenomeKmerCounts
GetMutationLoadsFromMutectVCFs	GetMutationLoadsFromMutectVCFs
GetMutationLoadsFromStrelkaIDVCFs	GetMutationLoadsFromStrelkaIDVCFs
GetMutationLoadsFromStrelkaSBSVCFs	GetMutationLoadsFromStrelkaSBSVCFs
GetMutectVAF	GetVAF
GetSequenceKmerCounts	GetSequenceKmerCounts
GetStrandedKmerCounts	GetStrandedKmerCounts
GetStrelkaVAF	GetVAF
GetVAF	GetVAF
ICAMS	ICAMS
InferAbundance	InferAbundance
InferCatalogClassPrefix	InferCatalogClassPrefix
InferCatalogInfo	InferCatalogInfo
InferRownames	InferRownames
IsGRCh37	IsGRCh37
IsGRCh38	IsGRCh38
IsGRCm38	IsGRCm38
MakeDataFrameFromVCF	MakeDataFrameFromVCF
MakeVCFDBSdf	MakeVCFDBSdf
MutectVCFFilesToCatalog	MutectVCFFilesToCatalog
MutectVCFFilesToCatalogAndPlotToPdf	MutectVCFFilesToCatalogAndPlotToPdf
MutectVCFFilesToZipFile	MutectVCFFilesToZipFile
NormalizeGenomeArg	NormalizeGenomeArg
Plot96PartOfCompositeToPDF	Plot96PartOfCompositeToPDF
PlotCatalog	PlotCatalog
PlotCatalogToPdf	PlotCatalogToPdf
PlotPPM	PlotPPM
PlotPPMToPdf	PlotPPMToPdf
PlotTransBiasGeneExp	PlotTransBiasGeneExp
PlotTransBiasGeneExpToPdf	PlotTransBiasGeneExpToPdf
ReadAndSplitMutectVCFs	ReadAndSplitMutectVCFs
ReadAndSplitStrelkaSBSVCFs	ReadAndSplitStrelkaSBSVCFs
ReadAndSplitVCFs	ReadAndSplitVCFs
ReadBedRanges	ReadBedRanges
ReadCatalog	ReadCatalog
ReadCatalogErrReturn	ReadCatalogErrReturn
ReadCatalogInternal	ReadCatalogInternal
ReadDukeNUSCat192	ReadDukeNUSCat192
ReadMutectVCF	ReadMutectVCF
ReadMutectVCFs	ReadMutectVCFs
ReadStapleGT96SBS	ReadStapleGT96SBS
ReadStrelkaIDVCF	ReadStrelkaIDVCF
ReadStrelkaIDVCFs	ReadStrelkaIDVCFs
ReadStrelkaSBSVCF	ReadStrelkaSBSVCF
ReadStrelkaSBSVCFs	ReadStrelkaSBSVCFs
ReadTranscriptRanges	ReadTranscriptRanges
ReadVCF	ReadVCF
ReadVCFs	ReadVCFs
RemoveRangesOnBothStrand	RemoveRangesOnBothStrand
RenameColumnsWithNameStrand	RenameColumnsWithNameStrand
RenameColumnsWithNameVAF	RenameColumnsWithNameVAF
Restaple1536	Restaple1536
Restaple96	Restaple96
revc	revc
RevcDBS144	RevcDBS144
RevcSBS96	RevcSBS96
SplitListOfMutectVCFs	SplitListOfMutectVCFs
SplitListOfStrelkaSBSVCFs	SplitListOfStrelkaSBSVCFs
SplitListOfVCFs	SplitListOfVCFs
SplitOneMutectVCF	SplitOneMutectVCF
SplitOneVCF	SplitOneVCF
SplitSBSVCF	SplitSBSVCF
SplitStrelkaSBSVCF	SplitStrelkaSBSVCF
StandardChromName	StandardChromName
StandardChromNameNew	StandardChromNameNew
StopIfCatalogTypeIllegal	StopIfCatalogTypeIllegal
StopIfNrowIllegal	StopIfNrowIllegal
StopIfRegionIllegal	StopIfRegionIllegal
StopIfTranscribedRegionIllegal	StopIfTranscribedRegionIllegal
StrelkaIDVCFFilesToCatalog	StrelkaIDVCFFilesToCatalog
StrelkaIDVCFFilesToCatalogAndPlotToPdf	StrelkaIDVCFFilesToCatalogAndPlotToPdf
StrelkaIDVCFFilesToZipFile	StrelkaIDVCFFilesToZipFile
StrelkaSBSVCFFilesToCatalog	StrelkaSBSVCFFilesToCatalog
StrelkaSBSVCFFilesToCatalogAndPlotToPdf	StrelkaSBSVCFFilesToCatalogAndPlotToPdf
StrelkaSBSVCFFilesToZipFile	StrelkaSBSVCFFilesToZipFile
TCFromCouSigCou	TCFromCouSigCou
TCFromDenSigDen	TCFromDenSigDen
TestMakeCatalogFromMutectVCFs	TestMakeCatalogFromMutectVCFs
TestMakeCatalogFromStrelkaIDVCFs	TestMakeCatalogFromStrelkaIDVCFs
TestMakeCatalogFromStrelkaSBSVCFs	TestMakeCatalogFromStrelkaSBSVCFs
TestPlotCatCOMPOSITE	TestPlotCatCOMPOSITE
trans.ranges.GRCh37	TranscriptRanges
trans.ranges.GRCh38	TranscriptRanges
trans.ranges.GRCm38	TranscriptRanges
TranscriptRanges	TranscriptRanges
TransformCatalog	TransformCatalog
TransRownames.ID.PCAWG.SigPro	TransRownames.ID.PCAWG.SigPro
TransRownames.ID.SigPro.PCAWG	TransRownames.ID.SigPro.PCAWG
Unstaple1536	Unstaple1536
Unstaple78	Unstaple78
Unstaple96	Unstaple96
VCFsToCatalogs	VCFsToCatalogs
VCFsToCatalogsAndPlotToPdf	VCFsToCatalogsAndPlotToPdf
VCFsToDBSCatalogs	VCFsToDBSCatalogs
VCFsToIDCatalogs	VCFsToIDCatalogs
VCFsToSBSCatalogs	VCFsToSBSCatalogs
VCFsToZipFile	VCFsToZipFile
VCFsToZipFileXtra	VCFsToZipFileXtra
WriteCat	WriteCat
WriteCatalog	WriteCatalog
WriteCatalogIndelSigPro	WriteCatalogIndelSigPro
