API for cgab-ncc/FIREVAT
FIREVAT, FInding REliable Variants without ArTifacts
| Global functions | |
|---|---|
| .onAttach | Source code |
| AND.multiple | Man page |
| AnnotateVCFObj | Man page Source code |
| CheckIfVariantRefinementIsNecessary | Man page Source code |
| Chromosome.Names | Man page |
| ComputeZScore | Man page Source code |
| ComputeZScoreEquiValue | Man page Source code |
| DecimalCeiling | Man page Source code |
| Default.Obj.Fn | Man page Source code |
| DefaultFilterToBinary | Man page Source code |
| EnumerateTriNucCounts | Man page Source code |
| Euc.Exp.Weighted.Obj.Fn | Man page Source code |
| Euc.Exp.Weighted.Seq.Art.Only.Obj.Fn.1 | Man page Source code |
| Euc.Exp.Weighted.Seq.Art.Only.Obj.Fn.2 | Man page Source code |
| Euc.Obj.Fn | Man page Source code |
| Exp.Weighted.A.Art.Obj.Fn | Man page Source code |
| Exp.Weighted.A.Ref.Obj.Fn | Man page Source code |
| Exp.Weighted.Obj.Fn.1 | Man page Source code |
| Exp.Weighted.Obj.Fn.2 | Man page Source code |
| Exp.Weighted.Refined.Seq.Art.Only.Obj.Fn | Man page Source code |
| FIREVATStartupMessage | Source code |
| FilterByStrandBiasAnalysis | Man page Source code |
| FilterVCF | Man page Source code |
| GADecodeBinaryString | Man page Source code |
| GAMonitorFn | Man page Source code |
| GAOptimizationObjFn | Man page Source code |
| GAOptimizationObjFnHelper | Man page Source code |
| GenerateConfigObj | Man page Source code |
| GetCOSMICMutSigs | Man page Source code |
| GetCOSMICMutSigsEtiologiesColors | Man page Source code |
| GetCOSMICMutSigsNames | Man page Source code |
| GetGASuggestedSolutions | Man page Source code |
| GetOptimizedSignatures | Man page Source code |
| GetPCAWGMutSigs | Man page Source code |
| GetPCAWGMutSigsEtiologiesColors | Man page Source code |
| GetPCAWGMutSigsNames | Man page Source code |
| GetPCAWGPlatinumMutSigs | Man page Source code |
| GetPCAWGPlatinumMutSigsEtiologiesColors | Man page Source code |
| GetPCAWGPlatinumMutSigsNames | Man page Source code |
| GetParameterLowerUpperVector | Man page Source code |
| GetSeedForVCF | Man page Source code |
| GetVCFValues | Man page Source code |
| InitializeVCF | Man page Source code |
| Leaky.ReLU.A.Art.Obj.Fn | Man page Source code |
| Leaky.ReLU.A.Ref.Obj.Fn | Man page Source code |
| Leaky.ReLU.Obj.Fn | Man page Source code |
| MakeFilter | Man page Source code |
| MatchINFOKeyValue | Man page Source code |
| MutPatParseRefMutSigs | Man page Source code |
| MutPatParseVCFObj | Man page Source code |
| MutaliskParseVCFObj | Man page Source code |
| MutaliskSigIndicesToNames | Man page Source code |
| MutaliskSigNamesToIndices | Man page Source code |
| OR.multiple | Man page |
| PCAWG.All.Sequencing.Artifact.Signatures | Man page |
| PCAWG.Known.Sequencing.Artifact.Signatures | Man page |
| PCAWG.Platinum.All.Technology.Related.Artifact.Signatures | Man page |
| PCAWG.Possible.Sequencing.Artifact.Signatures | Man page |
| PCAWG.Target.Mutational.Signatures | Man page |
| ParameterToBits | Man page Source code |
| ParseConfigFile | Man page Source code |
| PerformStrandBiasAnalysis | Man page Source code |
| PlotMutaliskResults | Man page Source code |
| PlotMutationTypes | Man page Source code |
| PlotOptimizationIterations | Man page Source code |
| PlotSignaturesContProbs | Man page Source code |
| PlotTable | Man page Source code |
| PlotTriNucSpectrum | Man page Source code |
| PlotVCFStatsBoxPlots | Man page Source code |
| PlotVCFStatsHistograms | Man page Source code |
| PrepareAnnotationDB | Man page Source code |
| PrepareArtifactAnnotationTable | Man page Source code |
| PrepareArtifactStrandBiasTable | Man page Source code |
| PrepareArtifactualMutsOptimizationIterationsPlot | Man page Source code |
| PrepareFilterCutoffsTable | Man page Source code |
| PrepareGeneticAlgorithmParametersTable | Man page Source code |
| PrepareIdentifiedSignaturesPlot | Man page Source code |
| PrepareIdentifiedSignaturesPlotHelper | Man page Source code |
| PrepareMLEReconstructedSpectrumsPlot | Man page Source code |
| PrepareNucleotideSubstitutionTypesPlot | Man page Source code |
| PrepareObservedSpectrumsPlot | Man page Source code |
| PrepareOptimizationResultsTable | Man page Source code |
| PrepareOptimizedVCFStatisticsPlot | Man page Source code |
| PrepareRefinedAnnotationTable | Man page Source code |
| PrepareRefinedMutsOptimizationIterationsPlot | Man page Source code |
| PrepareRefinedStrandBiasTable | Man page Source code |
| PrepareResidualSpectrumsPlot | Man page Source code |
| PrepareTrinucleotideSpectrumsTable | Man page Source code |
| PrintLog | Man page Source code |
| QueryAnnotatedVCF | Man page Source code |
| ReadOptimizationIterationReport | Man page Source code |
| ReadVCF | Man page Source code |
| ReportFIREVATResults | Man page Source code |
| RunFIREVAT | Man page Source code |
| RunGAMode | Man page Source code |
| RunManualMode | Man page Source code |
| RunMutPat | Man page Source code |
| RunMutalisk | Man page Source code |
| RunMutaliskHelper | Man page Source code |
| Sig.Extraction.Obj.Fn | Man page Source code |
| Sigmoid.Obj.Fn | Man page Source code |
| Test.Obj.Fn.1 | Man page Source code |
| Test.Obj.Fn.2 | Man page Source code |
| TransformValueType | Man page Source code |
| TriNuc.Mutation.Type.Hex.Colors | Man page |
| UpdateFilter | Man page Source code |
| WriteFIREVATResultsToTSV | Man page Source code |
| WriteVCF | Man page Source code |
