ICAMS
In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

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Functions
363
Source code
81
Man pages
164
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ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')
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API

API for ICAMS
In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Global functions
AbundanceIsSame Source code
AddAndCheckDBSClassInVCF Man page
AddAndCheckSBSClassInVCF Man page
AddDBSClass Man page
AddRunInformation Man page Source code
AddSBSClass Man page
AddSeqContext Man page
AddTranscript Man page
AnnotateDBSVCF Man page
AnnotateIDVCF Man page Source code
AnnotateSBSVCF Man page
CalBaseCountsFrom3MerAbundance Man page
CalculateExpressionLevel Source code
CalculateNumberOfSpace Man page Source code
CalculatePValues Source code
Canonicalize1Del Man page Source code
Canonicalize1ID Man page Source code
Canonicalize1INS Man page Source code
CanonicalizeID Man page Source code
CatalogRowOrder Man page
CheckAndFixChrNames Man page Source code
CheckAndFixChrNamesForTransRanges Man page Source code
CheckAndNormalizeTranCatArgs Source code
CheckAndRemoveDiscardedVariants Source code
CheckAndReorderRownames Man page
CheckAndReturnDBSCatalogs Man page Source code
CheckAndReturnDBSMatrix Man page
CheckAndReturnIDCatalog Man page Source code
CheckAndReturnIDMatrix Man page Source code
CheckAndReturnSBSCatalogs Man page Source code
CheckAndReturnSBSMatrix Man page
CheckCatalogAttributes Source code
CheckDBSClassInVCF Man page
CheckSBSClassInVCF Man page
CheckSeqContextInVCF Man page
Collapse144AbundanceTo78 Source code
Collapse144CatalogTo78 Man page Source code
Collapse1536CatalogTo96 Man page Source code
Collapse192AbundanceTo96 Source code
Collapse192CatalogTo96 Man page Source code
Collapse5bpAbundanceTo3bp Source code
CollapseCatalog Man page
CombineAndReturnCatalogsForMutectVCFs Source code
CombineAndReturnCatalogsForStrelkaSBSVCFs Source code
CombineAndReturnCatalogsForVCFs Source code
ConvertCatalogToSigProfilerFormat Man page Source code
ConvertICAMSCatalogToSigProSBS96 Man page Source code
CreateDinucAbundance Man page
CreateExomeStrandedRanges Man page
CreateOneColDBSMatrix Man page
CreateOneColIDMatrix Man page Source code
CreateOneColSBSMatrix Man page
CreateOnePPMFromSBSVCF Man page Source code
CreatePPMFromSBSVCFs Man page Source code
CreatePentanucAbundance Man page
CreateStrandedDinucAbundance Man page
CreateStrandedTrinucAbundance Man page
CreateTetranucAbundance Man page
CreateTransRanges Man page Source code
CreateTrinucAbundance Man page
DefaultFilterStatus Source code
FindDelMH Man page Source code
FindMaxRepeatDel Man page Source code
FindMaxRepeatIns Man page Source code
GeneExpressionData Man page
GenerateEmptyKmerCounts Man page
GenerateKmer Man page
GeneratePCAWGAliquotID2 Source code
GeneratePlotPFMmatrix Man page Source code
GenerateVCFsFromIndelSimpleFile1 Man page Source code
GenerateVCFsFromIndelSimpleFiles Man page Source code
Get1BPIndelFlanks Man page Source code
GetCustomKmerCounts Man page
GetFreebayesVAF Man page Source code
GetGenomeKmerCounts Man page
GetMutationLoadsFromMutectVCFs Man page Source code
GetMutationLoadsFromStrelkaIDVCFs Man page Source code
GetMutationLoadsFromStrelkaSBSVCFs Man page Source code
GetMutectVAF Man page Source code
GetPCAWGConsensusVAF Man page Source code
GetSequenceKmerCounts Man page
GetStrandedKmerCounts Man page
GetStrelkaVAF Man page Source code
GetVAF Man page
HaplotypePlot Man page Source code
ICAMS Man page
InferAbundance Man page
InferCatalogClassPrefix Man page Source code
InferCatalogClassString Source code
InferCatalogInfo Man page Source code
InferRefGenomeName Man page
InferRownames Man page Source code
IsCounts Source code
IsDensity Source code
IsGRCh37 Man page
IsGRCh38 Man page
IsGRCm38 Man page
IsICAMSCatalog Man page Source code Source code
IsRefGenomeInstalled Man page Source code
IsSignature Source code
IsTransformationLegal Source code
Make96Catalog Source code
MakeCOMPOSITECatalog Source code
MakeCOMPOSITECatalogFromICAMSExt Source code
MakeDBS136Catalog Source code
MakeDBS136CatalogFromICAMSExt Source code
MakeDBS144Catalog Source code
MakeDBS144CatalogFromICAMSExt Source code
MakeDBS78Catalog Source code
MakeDBS78CatalogFromICAMSExt Source code
MakeDBS78CatalogFromSigPro Source code
MakeDataFrameFromVCF Man page Source code
MakeID166Catalog Source code
MakeID83Catalog Source code
MakeID83CatalogFromICAMSExt Source code
MakeID83CatalogFromSigPro Source code
MakeID83ICAMSFromSigProID96 Source code
MakeSBS1536Catalog Source code
MakeSBS1536CatalogFromICAMSExt Source code
MakeSBS1536CatalogFromSigPro Source code
MakeSBS192Catalog Source code
MakeSBS192CatalogFromICAMSExt Source code
MakeSBS96CatalogFromICAMSExt Source code
MakeSBS96CatalogFromSigPro Source code
MakeVCFDBSdf Man page
MutectVCFFilesToCatalog Man page Source code
MutectVCFFilesToCatalogAndPlotToPdf Man page
MutectVCFFilesToZipFile Man page Source code
NormalizeGenomeArg Man page
Plot96PartOfCompositeToPDF Man page Source code
PlotCatalog Man page Source code
PlotCatalog.DBS136Catalog Source code
PlotCatalog.DBS144Catalog Source code
PlotCatalog.DBS78Catalog Source code
PlotCatalog.ID166Catalog Source code
PlotCatalog.IndelCatalog Source code
PlotCatalog.SBS1536Catalog Source code
PlotCatalog.SBS192Catalog Source code
PlotCatalog.SBS96Catalog Source code
PlotCatalogToPdf Man page Source code
PlotCatalogToPdf.DBS136Catalog Source code
PlotCatalogToPdf.DBS144Catalog Source code
PlotCatalogToPdf.DBS78Catalog Source code
PlotCatalogToPdf.ID166Catalog Source code
PlotCatalogToPdf.IndelCatalog Source code
PlotCatalogToPdf.SBS1536Catalog Source code
PlotCatalogToPdf.SBS192Catalog Source code
PlotCatalogToPdf.SBS96Catalog Source code
PlotPFMmatrix Man page Source code
PlotPPM Man page Source code
PlotPPMToPdf Man page Source code
PlotStrandBiasColorMatrix Source code
PlotTransBiasGeneExp Man page Source code
PlotTransBiasGeneExpToPdf Man page Source code
ReadAndSplitMutectVCFs Man page Source code
ReadAndSplitStrelkaSBSVCFs Man page Source code
ReadAndSplitVCFs Man page Source code
ReadBedRanges Man page
ReadCatalog Man page Source code
ReadCatalogErrReturn Man page Source code
ReadCatalogInternal Man page Source code
ReadDukeNUSCat192 Man page Source code
ReadMutectVCF Man page Source code
ReadMutectVCFs Man page
ReadStapleGT96SBS Man page Source code
ReadStrelkaIDVCF Man page Source code
ReadStrelkaIDVCFs Man page Source code
ReadStrelkaSBSVCF Man page Source code
ReadStrelkaSBSVCFs Man page
ReadTranscriptRanges Man page
ReadVCF Man page Source code
ReadVCFs Man page Source code
RefGenomeIsSame Source code
RegionIsSame Source code
RemoveRangesOnBothStrand Man page
RemoveRowsWithDuplicatedCHROMAndPOS Source code
RemoveRowsWithDuplicatedCHROMAndPOSNew Source code
RemoveRowsWithPoundSign Source code
RemoveRowsWithPoundSignNew Source code
RenameColumnsWithNameEnd Man page Source code
RenameColumnsWithNameStart Man page Source code
RenameColumnsWithNameStrand Man page Source code
RenameColumnsWithNameVAF Man page Source code
Restaple1536 Man page Source code
Restaple96 Man page Source code
RevcDBS144 Man page
RevcSBS96 Man page
SelectVariantsByChromName Man page Source code
SimpleReadVCF Man page Source code
SplitCatCOMPOSITE Source code
SplitListOfMutectVCFs Man page Source code
SplitListOfStrelkaSBSVCFs Man page
SplitListOfVCFs Man page
SplitOneMutectVCF Man page Source code
SplitOneVCF Man page
SplitSBSVCF Man page Source code
SplitStrelkaSBSVCF Man page
StandardChromName Man page Source code
StandardChromNameNew Man page Source code
StopIfCatalogTypeIllegal Man page
StopIfNrowIllegal Man page
StopIfRegionIllegal Man page
StopIfTranscribedRegionIllegal Man page
StrandBiasGeneExp Source code
StrelkaIDVCFFilesToCatalog Man page Source code
StrelkaIDVCFFilesToCatalogAndPlotToPdf Man page
StrelkaIDVCFFilesToZipFile Man page Source code
StrelkaSBSVCFFilesToCatalog Man page Source code
StrelkaSBSVCFFilesToCatalogAndPlotToPdf Man page
StrelkaSBSVCFFilesToZipFile Man page Source code
SymmetricalContextsFor1BPIndel Man page Source code
TCFromCou Source code
TCFromCouSig Source code
TCFromCouSigCou Man page Source code
TCFromDenSigDen Man page Source code
TestMakeCatalogFromMutectVCFs Man page Source code
TestMakeCatalogFromStrelkaIDVCFs Man page Source code
TestMakeCatalogFromStrelkaSBSVCFs Man page Source code
TestPlotCatCOMPOSITE Man page Source code
TransRownames.ID.PCAWG.SigPro Man page Source code
TransRownames.ID.SigPro.PCAWG Man page Source code
TranscriptRanges Man page
TransformCatalog Man page Source code
Unstaple1536 Man page Source code
Unstaple78 Man page Source code
Unstaple96 Man page Source code
VCFsToCatalogs Man page Source code
VCFsToCatalogsAndPlotToPdf Man page
VCFsToDBSCatalogs Man page Source code
VCFsToIDCatalogs Man page Source code
VCFsToSBSCatalogs Man page Source code
VCFsToZipFile Man page Source code
VCFsToZipFileXtra Man page Source code
WriteCat Man page Source code
WriteCatalog Man page Source code
WriteCatalog.COMPOSITECatalog Source code
WriteCatalog.DBS136Catalog Source code
WriteCatalog.DBS144Catalog Source code
WriteCatalog.DBS78Catalog Source code
WriteCatalog.ID166Catalog Source code
WriteCatalog.IndelCatalog Source code
WriteCatalog.SBS1536Catalog Source code
WriteCatalog.SBS192Catalog Source code
WriteCatalog.SBS96Catalog Source code
WriteCatalogIndelSigPro Man page Source code
WriteSBS96CatalogAsTsv Source code
all.abundance Man page
as.catalog Man page
catalog.row.order Man page
gene.expression.data.HepG2 Man page
gene.expression.data.MCF10A Man page
revc Man page
revcSBS6 Source code
trans.ranges.GRCh37 Man page
trans.ranges.GRCh38 Man page
trans.ranges.GRCm38 Man page
ICAMS documentation built on June 15, 2025, 1:08 a.m.

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