cgab-ncc/FIREVAT
FIREVAT, FInding REliable Variants without ArTifacts

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cgab-ncc/FIREVAT: FIREVAT, FInding REliable Variants without ArTifacts
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Man pages for cgab-ncc/FIREVAT
FIREVAT, FInding REliable Variants without ArTifacts

AND.multipleAND.multiple
AnnotateVCFObjAnnotateVCFObj
CheckIfVariantRefinementIsNecessaryCheckIfVariantRefinementIsNecessary
Chromosome.NamesConstant
ComputeZScoreComputeZScore
ComputeZScoreEquiValueComputeZScoreEquiValue
DecimalCeilingDecimalCeiling
DefaultFilterToBinaryTransform default filtering parameters to a binary vector
Default.Obj.FnDefault.Obj.Fn
EnumerateTriNucCountsEnumerateTriNucCounts
Euc.Exp.Weighted.Obj.FnEuc.Exp.Weighted.Obj.Fn
Euc.Exp.Weighted.Seq.Art.Only.Obj.Fn.1Euc.Exp.Weighted.Seq.Art.Only.Obj.Fn.1
Euc.Exp.Weighted.Seq.Art.Only.Obj.Fn.2Euc.Exp.Weighted.Seq.Art.Only.Obj.Fn.2
Euc.Obj.FnEuc.Obj.Fn
Exp.Weighted.A.Art.Obj.FnExp.Weighted.A.Art.Obj.Fn
Exp.Weighted.A.Ref.Obj.FnExp.Weighted.A.Ref.Obj.Fn
Exp.Weighted.Obj.Fn.1Exp.Weighted.Obj.Fn.1
Exp.Weighted.Obj.Fn.2Exp.Weighted.Obj.Fn.2
Exp.Weighted.Refined.Seq.Art.Only.Obj.FnExp.Weighted.Refined.Seq.Art.Only.Obj.Fn
FilterByStrandBiasAnalysisFilterByStrandBiasAnalysis
FilterVCFFilterVCF
GADecodeBinaryStringGADecodeBinaryString
GAMonitorFnGAMonitorFn
GAOptimizationObjFnGAOptimizationObjFn
GAOptimizationObjFnHelperGAOptimizationObjFnHelper
GenerateConfigObjGenerate config.obj by checking vcf header
GetCOSMICMutSigsGetCOSMICMutSigs
GetCOSMICMutSigsEtiologiesColorsGetCOSMICMutSigsNames
GetCOSMICMutSigsNamesGetCOSMICMutSigsNames
GetGASuggestedSolutionsGetGASuggestedSolutions
GetOptimizedSignaturesGetOptimizedSignatures
GetParameterLowerUpperVectorGetParameterLowerUpperVector
GetPCAWGMutSigsGetPCAWGMutSigs
GetPCAWGMutSigsEtiologiesColorsGetPCAWGMutSigsEtiologiesColors
GetPCAWGMutSigsNamesGetPCAWGMutSigsNames
GetPCAWGPlatinumMutSigsGetPCAWGPlatinumMutSigs
GetPCAWGPlatinumMutSigsEtiologiesColorsGetPCAWGPlatinumMutSigsEtiologiesColors
GetPCAWGPlatinumMutSigsNamesGetPCAWGPlatinumMutSigsNames
GetSeedForVCFGetSeedForVCF
GetVCFValuesGetVCFValues
InitializeVCFInitializeVCF
Leaky.ReLU.A.Art.Obj.FnLeaky.ReLU.A.Art.Obj.Fn
Leaky.ReLU.A.Ref.Obj.FnLeaky.ReLU.A.Ref.Obj.Fn
Leaky.ReLU.Obj.FnLeaky.ReLU.Obj.Fn
MakeFilterMakeFilter
MatchINFOKeyValueAn internal function for parsing INFO column.
MutaliskParseVCFObjMutaliskParseVCFObj
MutaliskSigIndicesToNamesMutaliskSigIndicesToNames
MutaliskSigNamesToIndicesMutaliskSigNamesToIndices
MutPatParseRefMutSigsMutPatParseRefMutSigs
MutPatParseVCFObjMutPatParseVCFObj
OR.multipleOR.multiple
ParameterToBitsParameterToBits
ParseConfigFileParseConfigFile
PCAWG.All.Sequencing.Artifact.SignaturesConstant
PCAWG.Known.Sequencing.Artifact.SignaturesConstant
PCAWG.Platinum.All.Technology.Related.Artifact.SignaturesConstant
PCAWG.Possible.Sequencing.Artifact.SignaturesConstant
PCAWG.Target.Mutational.SignaturesConstant
PerformStrandBiasAnalysisPerformStrandBiasAnalysis
PlotMutaliskResultsPlotMutaliskResults
PlotMutationTypesPlotMutationTypes
PlotOptimizationIterationsPlotOptimizationIterations
PlotSignaturesContProbsPlotSignaturesContProbs
PlotTablePlotTable
PlotTriNucSpectrumPlotTriNucSpectrum
PlotVCFStatsBoxPlotsPlotVCFStatsBoxPlots
PlotVCFStatsHistogramsPlotVCFStatsHistograms
PrepareAnnotationDBPrepareAnnotationDB
PrepareArtifactAnnotationTablePrepareArtifactAnnotationTable
PrepareArtifactStrandBiasTablePrepareArtifactStrandBiasTable
PrepareArtifactualMutsOptimizationIterationsPlotPrepareArtifactualMutsOptimizationIterationsPlot
PrepareFilterCutoffsTablePrepareFilterCutoffsTable
PrepareGeneticAlgorithmParametersTablePrepareGeneticAlgorithmParametersTable
PrepareIdentifiedSignaturesPlotPrepareIdentifiedSignaturesPlot
PrepareIdentifiedSignaturesPlotHelperPrepareIdentifiedSignaturesPlotHelper
PrepareMLEReconstructedSpectrumsPlotPrepareMLEReconstructedSpectrumsPlot
PrepareNucleotideSubstitutionTypesPlotPrepareNucleotideSubstitutionTypesPlot
PrepareObservedSpectrumsPlotPrepareObservedSpectrumsPlot
PrepareOptimizationResultsTablePrepareOptimizationResultsTable
PrepareOptimizedVCFStatisticsPlotPrepareOptimizedVCFStatisticsPlot
PrepareRefinedAnnotationTablePrepareRefinedAnnotationTable
PrepareRefinedMutsOptimizationIterationsPlotPrepareRefinedMutsOptimizationIterationsPlot
PrepareRefinedStrandBiasTablePrepareRefinedStrandBiasTable
PrepareResidualSpectrumsPlotPrepareResidualSpectrumsPlot
PrepareTrinucleotideSpectrumsTablePrepareTrinucleotideSpectrumsTable
PrintLogPrintLog
QueryAnnotatedVCFFilterAnnotatedVCF
ReadOptimizationIterationReportReadOptimizationIterationReport
ReadVCFReadVCF
ReportFIREVATResultsReportFIREVATResults
RunFIREVATRunFIREVAT
RunGAModeRunGAMode
RunManualModeRunManualMode
RunMutaliskRunMutalisk
RunMutaliskHelperRunMutaliskHelper
RunMutPatRunMutPat
Sig.Extraction.Obj.FnSig.Extraction.Obj.Fn
Sigmoid.Obj.FnSigmoid.Obj.Fn
Test.Obj.Fn.1Test.Obj.Fn.1
Test.Obj.Fn.2Test.Obj.Fn.2
TransformValueTypeTransformValueType
TriNuc.Mutation.Type.Hex.ColorsConstant
UpdateFilterUpdateFilter
WriteFIREVATResultsToTSVWriteFIREVATResultsToTSV
WriteVCFWriteVCF
cgab-ncc/FIREVAT documentation built on Nov. 19, 2022, 5:55 p.m.

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