Files in cgab-ncc/FIREVAT

FIREVAT, FInding REliable Variants without ArTifacts

LICENSE.md R/firevat_annotation.R R/firevat_brute_force.R R/firevat_config.R R/firevat_constants.R R/firevat_filter.R R/firevat_log.R R/firevat_main.R R/firevat_maths.R R/firevat_mutalisk.R R/firevat_mutational_patterns.R R/firevat_objective_functions.R R/firevat_optimization.R R/firevat_plot.R R/firevat_report.R R/firevat_strand_bias.R R/firevat_utils.R R/firevat_vcf.R R/zzz.R README.md docs/FIREVAT_0.6.0.pdf examples/firevat_run_example.R examples/firevat_run_example_with_annotation.R examples/firevat_run_manual_filter.R inst/extdata/PCAWG_sigProfiler_SBS_vignettes_20180514.pdf inst/extdata/PCAWG_sigProfiler_exome_SBS_signatures_20180321.pdf inst/extdata/PCAWG_sigProfiler_genome_SBS_signatures_20180321.pdf inst/rmd_template/report_ga.Rmd inst/rmd_template/report_manual.Rmd man/AND.multiple.Rd man/AnnotateVCFObj.Rd man/CheckIfVariantRefinementIsNecessary.Rd man/Chromosome.Names.Rd man/ComputeZScore.Rd man/ComputeZScoreEquiValue.Rd man/DecimalCeiling.Rd man/Default.Obj.Fn.Rd man/DefaultFilterToBinary.Rd man/EnumerateTriNucCounts.Rd man/Euc.Exp.Weighted.Obj.Fn.Rd man/Euc.Exp.Weighted.Seq.Art.Only.Obj.Fn.1.Rd man/Euc.Exp.Weighted.Seq.Art.Only.Obj.Fn.2.Rd man/Euc.Obj.Fn.Rd man/Exp.Weighted.A.Art.Obj.Fn.Rd man/Exp.Weighted.A.Ref.Obj.Fn.Rd man/Exp.Weighted.Obj.Fn.1.Rd man/Exp.Weighted.Obj.Fn.2.Rd man/Exp.Weighted.Refined.Seq.Art.Only.Obj.Fn.Rd man/FilterByStrandBiasAnalysis.Rd man/FilterVCF.Rd man/GADecodeBinaryString.Rd man/GAMonitorFn.Rd man/GAOptimizationObjFn.Rd man/GAOptimizationObjFnHelper.Rd man/GenerateConfigObj.Rd man/GetCOSMICMutSigs.Rd man/GetCOSMICMutSigsEtiologiesColors.Rd man/GetCOSMICMutSigsNames.Rd man/GetGASuggestedSolutions.Rd man/GetOptimizedSignatures.Rd man/GetPCAWGMutSigs.Rd man/GetPCAWGMutSigsEtiologiesColors.Rd man/GetPCAWGMutSigsNames.Rd man/GetPCAWGPlatinumMutSigs.Rd man/GetPCAWGPlatinumMutSigsEtiologiesColors.Rd man/GetPCAWGPlatinumMutSigsNames.Rd man/GetParameterLowerUpperVector.Rd man/GetSeedForVCF.Rd man/GetVCFValues.Rd man/InitializeVCF.Rd man/Leaky.ReLU.A.Art.Obj.Fn.Rd man/Leaky.ReLU.A.Ref.Obj.Fn.Rd man/Leaky.ReLU.Obj.Fn.Rd man/MakeFilter.Rd man/MatchINFOKeyValue.Rd man/MutPatParseRefMutSigs.Rd man/MutPatParseVCFObj.Rd man/MutaliskParseVCFObj.Rd man/MutaliskSigIndicesToNames.Rd man/MutaliskSigNamesToIndices.Rd man/OR.multiple.Rd man/PCAWG.All.Sequencing.Artifact.Signatures.Rd man/PCAWG.Known.Sequencing.Artifact.Signatures.Rd man/PCAWG.Platinum.All.Technology.Related.Artifact.Signatures.Rd man/PCAWG.Possible.Sequencing.Artifact.Signatures.Rd man/PCAWG.Target.Mutational.Signatures.Rd man/ParameterToBits.Rd man/ParseConfigFile.Rd man/PerformStrandBiasAnalysis.Rd man/PlotMutaliskResults.Rd man/PlotMutationTypes.Rd man/PlotOptimizationIterations.Rd man/PlotSignaturesContProbs.Rd man/PlotTable.Rd man/PlotTriNucSpectrum.Rd man/PlotVCFStatsBoxPlots.Rd man/PlotVCFStatsHistograms.Rd man/PrepareAnnotationDB.Rd man/PrepareArtifactAnnotationTable.Rd man/PrepareArtifactStrandBiasTable.Rd man/PrepareArtifactualMutsOptimizationIterationsPlot.Rd man/PrepareFilterCutoffsTable.Rd man/PrepareGeneticAlgorithmParametersTable.Rd man/PrepareIdentifiedSignaturesPlot.Rd man/PrepareIdentifiedSignaturesPlotHelper.Rd man/PrepareMLEReconstructedSpectrumsPlot.Rd man/PrepareNucleotideSubstitutionTypesPlot.Rd man/PrepareObservedSpectrumsPlot.Rd man/PrepareOptimizationResultsTable.Rd man/PrepareOptimizedVCFStatisticsPlot.Rd man/PrepareRefinedAnnotationTable.Rd man/PrepareRefinedMutsOptimizationIterationsPlot.Rd man/PrepareRefinedStrandBiasTable.Rd man/PrepareResidualSpectrumsPlot.Rd man/PrepareTrinucleotideSpectrumsTable.Rd man/PrintLog.Rd man/QueryAnnotatedVCF.Rd man/ReadOptimizationIterationReport.Rd man/ReadVCF.Rd man/ReportFIREVATResults.Rd man/RunFIREVAT.Rd man/RunGAMode.Rd man/RunManualMode.Rd man/RunMutPat.Rd man/RunMutalisk.Rd man/RunMutaliskHelper.Rd man/Sig.Extraction.Obj.Fn.Rd man/Sigmoid.Obj.Fn.Rd man/Test.Obj.Fn.1.Rd man/Test.Obj.Fn.2.Rd man/TransformValueType.Rd man/TriNuc.Mutation.Type.Hex.Colors.Rd man/UpdateFilter.Rd man/WriteFIREVATResultsToTSV.Rd man/WriteVCF.Rd scripts/firevat_run.R vignettes/FIREVAT_Experimental_Objective_Functions.Rmd vignettes/Introduction_to_FIREVAT.Rmd