Files in afrangou/CleanCNA

Calling and recalling subclonal copy number using SNP and SNV information to provide a high quality set of copy number profiles.

R/AssessBBDPCRun.R R/AssessBBDPCRun_B.R R/AssessBBDPCRun_afterpeakcalling.R R/CNAsDriversComplexHeatmap.R R/CNAsDriversHeatmap.R R/CleanBedopsOutput.R R/CodeSegments.R R/CodeSegments_test.R R/CollateSubclones.R R/ComputePeaksVAF.R R/ComputePeaksVAF_nf.R R/ConvertImputeInputToBeagleInput.R R/ConvertSubclones.R R/CreateScriptDirsBeagle.R R/CreateScriptsDirs.R R/CreateScriptsDirsFixedParams.R R/CreateWGDScriptDirs.R R/FirstBB.R R/ForCohortSummaries.R R/GenerateDPinput.R R/GenerateDPinput_GeL_vcfs.R R/GenerateDPinput_standard_vcf.R R/GenerateDPinput_strelka_vcf.R R/GenerateDPinput_t2BamAC.R R/GenerateDPinput_t2BamAC_Beagle.R R/GenerateDPinput_t2BamAC_Beagle_nf.R R/GenomewideStackedBar.R R/GenomewideStackedBarPlot.R R/LabelGenomecov.R R/PassFail.R R/PrepDataForSummary.R R/PrepShapeIt2.R R/QualityControl.R R/QualityControl_CNAqc.R R/RunBeagle5.R R/RunDPClust.R R/RunDPClust_Beagle_NF.R R/RunShapeIt2.R R/SetUpRun2BBDPC.R R/WriteBeagleAsImpute.R R/call.peaks.R R/computed.expected.peak.loc.R R/read.segs.R R/read.snvs.R R/reestimate.purity.R README.md man/AssessBBDPCRun.Rd man/AssessBBDPCRun_B.Rd man/AssessBBDPCRun_afterpeakcalling.Rd man/CNAsDriversComplexHeatmap.Rd man/CNAsDriversHeatmapDendrogram.Rd man/CleanBedopsOutput.Rd man/CodeSegments.Rd man/CodeSegments_test.Rd man/CollateSubclones.Rd man/ComputePeaksVAF.Rd man/ComputePeaksVAF_nf.Rd man/ConvertImputeInputToBeagleInput.Rd man/CreateScriptsDirs.Rd man/CreateScriptsDirsBeagle.Rd man/CreateScriptsDirsFixedParams.Rd man/CreateWGDScriptDirs.Rd man/FirstBB.Rd man/GenerateDPinput.Rd man/GenerateDPinput_mutect_vcf.Rd man/GenerateDPinput_strelka_vcf.Rd man/GenerateDPinput_t2BamAC.Rd man/GenerateDPinput_t2BamAC_Beagle.R man/GenerateDPinput_t2BamAC_Beagle.Rd man/GenerateDPinput_t2BamAC_Beagle_nf.Rd man/GenerateDPinputt2BamAC_Beagle_nf.Rd man/GenomewideStackedBar.Rd man/GenomewideStackedBarPlot.Rd man/LabelGenomecov.Rd man/PassFail.Rd man/PrepDataForSummary.Rd man/PrepShapeIt2.Rd man/QualityControl_CNAqc.Rd man/RunBeagle5.Rd man/RunDPClust_Beagle_nf.Rd man/RunShapeIt2.Rd man/SetUpRun2BBDPC.Rd man/WriteBeagleAsImpute.Rd man/call.peaks.Rd man/computed.expected.peak.loc.Rd man/convertSubclonesSingleSample.Rd man/read.segs.Rd man/read.snvs.Rd man/reestimate.purity.Rd