API for afrangou/CleanCNA
Calling and recalling subclonal copy number using SNP and SNV information to provide a high quality set of copy number profiles.
| Global functions | |
|---|---|
| AssessBBDPCRun | Man page Source code |
| AssessBBDPCRun_B | Man page Source code |
| AssessBBDPCRun_afterpeakcalling | Man page Source code |
| CNAsDriversComplexHeatmap | Man page Source code |
| CNAsDriversHeatmapDendrogram | Man page Source code |
| CleanBedopsOutput | Man page Source code |
| CodeSegments | Man page Source code |
| CodeSegments_test | Man page Source code |
| CollateSubclones | Man page Source code |
| ComputePeaksVAF | Man page Source code |
| ComputePeaksVAF_nf | Man page Source code |
| ConvertImputeInputToBeagleInput.Rd | Man page |
| ConvertSubclones | Source code |
| ConvertSubclonesSingleSample | Man page |
| CreateScriptsDirs | Man page Man page Source code |
| CreateScriptsDirsBeagle | Man page |
| CreateScriptsDirsFixedParams | Man page Source code |
| CreateWGDScriptDirs | Man page |
| CreateWGDrun | Source code |
| GenerateDPinput | Man page Source code Source code |
| GenerateDPinput_mutect_vcf | Man page Source code |
| GenerateDPinput_strelka_vcf | Man page Source code |
| GenerateDPinput_t2BamAC | Man page Man page |
| GenerateDPinputt2BamAC | Source code |
| GenerateDPinputt2BamAC_Beagle | Source code |
| GenerateDPinputt2BamAC_Beagle_nf | Man page Man page Source code |
| GenomewideStackedBar | Man page Source code |
| GenomewideStackedBarPlot | Man page Source code |
| LabelGenomecov | Man page Source code |
| PassFail | Man page Source code |
| PrepDataForSummary | Man page |
| PrepShapeIt2 | Man page Source code |
| QualityControl_CNAqc | Man page |
| RunBeagle5 | Man page |
| RunDPClust | Man page Source code |
| RunDPClust_Beagle_nf | Man page Source code |
| RunShapeIt2 | Man page |
| SetUpRun2BBDPC | Man page Source code |
| WriteBeagleAsImpute | Man page |
| call.peaks | Man page Source code |
| compute.expected.peak.loc | Man page |
| computed.expected.peak.loc | Source code |
| convert.impute.input.to.beagle.input | Source code |
| estimate.dpclust.purity | Source code Source code |
| estimate.new.ploidy | Source code Source code |
| get.worst.filter | Source code Source code |
| larger.all.later.numbers | Source code Source code |
| log.message | Source code Source code |
| pastedot | Source code Source code |
| pasteu | Source code Source code |
| prepDataForSummary | Man page Source code |
| qc | Source code |
| qc_CNAqc | Source code |
| read.segs | Man page Source code |
| read.snvs | Man page Source code |
| reestimate.purity | Man page Source code |
| run.beagle5 | Source code |
| switch.ploidy.get.ploidy | Source code Source code |
| switch.ploidy.get.purity | Source code Source code |
| writebeagle.as.impute | Source code |
