Files in cgab-ncc/FIREVAT
FIREVAT, FInding REliable Variants without ArTifacts
.DS_Store
.Rbuildignore
.gitignore
DESCRIPTION
FIREVAT.Rproj
LICENSE.md
NAMESPACE
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/.DS_Store
docs/FIREVAT_0.6.0.pdf
docs/FIREVAT_Experimental_Objective_Functions.html
docs/HCC1954_FIREVAT_Outputs.zip
docs/HCC1954_FIREVAT_Report.html
docs/Introduction_to_FIREVAT.html
docs/Report_Components.xlsx
docs/index.html
examples/firevat_run_example.R
examples/firevat_run_example_with_annotation.R
examples/firevat_run_manual_filter.R
inst/.DS_Store
inst/config/GATK4_Mutect2_config.json
inst/config/MC3_Muse_filtering_params.json
inst/config/MC3_Mutect_filtering_params_Normal_Tumor.json
inst/config/MC3_Mutect_filtering_params_Tumor_Normal.json
inst/config/MC3_SomaticSniper_filtering_params.json
inst/config/MC3_Varscan_filtering_params.json
inst/config/MC3_broad_vcf_filtering_params.json
inst/config/MuTect2_Filtering_Params.json
inst/config/Muse_Filtering_Params.json
inst/config/PCAWG_DKFZ_Cell_Line_Filtering_Params.json
inst/config/SomaticSniper_Filtering_Params.json
inst/config/Strelka_Filtering_Params.json
inst/config/Varscan2_Filtering_Params.json
inst/extdata/COSMIC_Signatures.csv
inst/extdata/COSMIC_Signatures_Groups_Colors.csv
inst/extdata/DCC_PCAWG_Cell_Lines_HCC1143.vcf
inst/extdata/DCC_PCAWG_Cell_Lines_HCC1954.vcf
inst/extdata/PCAWG_Platinum_Signatures.csv
inst/extdata/PCAWG_Platinum_Signatures_Groups_Colors.csv
inst/extdata/PCAWG_Signatures_Groups_Colors.csv
inst/extdata/PCAWG_sigProfiler_SBS_vignettes_20180514.pdf
inst/extdata/PCAWG_sigProfiler_exome_SBS_signatures_20180321.csv
inst/extdata/PCAWG_sigProfiler_exome_SBS_signatures_20180321.pdf
inst/extdata/PCAWG_sigProfiler_genome_SBS_Signatures_20180328.csv
inst/extdata/PCAWG_sigProfiler_genome_SBS_signatures_20180321.pdf
inst/img/FIREVAT_Sample_HTML_Report_Screenshots.png
inst/img/FIREVAT_Suggested_Workflow.png
inst/img/FIREVAT_Workflow_Figure.png
inst/rmd_template/extLogo.html
inst/rmd_template/firevat.css
inst/rmd_template/firevat.min.css
inst/rmd_template/firevat_logo.png
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/.gitignore
vignettes/FIREVAT_Experimental_Objective_Functions.Rmd
vignettes/FIREVAT_Experimental_Objective_Functions.html
vignettes/Introduction_to_FIREVAT.Rmd
vignettes/Introduction_to_FIREVAT.html
vignettes/res/FIREVAT_GA_Parameters_Table.png
vignettes/res/FIREVAT_Mutalisk_Parameters_Table.png
vignettes/res/FIREVAT_Report_1.png
vignettes/res/FIREVAT_Report_10.png
vignettes/res/FIREVAT_Report_11.png
vignettes/res/FIREVAT_Report_12.png
vignettes/res/FIREVAT_Report_2.png
vignettes/res/FIREVAT_Report_3.png
vignettes/res/FIREVAT_Report_4.png
vignettes/res/FIREVAT_Report_5.png
vignettes/res/FIREVAT_Report_6.png
vignettes/res/FIREVAT_Report_7.png
vignettes/res/FIREVAT_Report_8.png
vignettes/res/FIREVAT_Report_9.png
