API for J0bbie/R2CPCT
Misc. functions to perform import and analysis of WGS and RNA-Seq samples
| Global functions | |
|---|---|
| GENCODE.v38 | Man page |
| GENCODE.v38.Exons | Man page |
| cleanSeqlevels | Man page Source code |
| detectEnrichmentOfMutants | Man page Source code |
| detectKataegis_OLD | Man page |
| determineMutationalBurden | Man page Source code |
| determineTiTv | Man page Source code |
| driverList | Man page |
| findCPCTCenter | Man page Source code |
| fitCustomMutSigs | Man page Source code |
| fitMutSigs | Man page Source code |
| generateCombinedReport | Man page Source code |
| importArriba | Man page Source code |
| importGISTIC2 | Man page Source code |
| importLINXFusions | Man page Source code |
| importPurityStatsPURPLE | Man page Source code |
| importSomaticCopynumberPURPLE | Man page Source code |
| importSomaticVariantsVEP | Man page Source code |
| importStructuralVariantsPURPLE | Man page Source code |
| importWGSOfCohort | Man page Source code |
| importWGSOfSample | Man page Source code |
| importdriverCatalogHMF | Man page Source code |
| initializeLogger | Man page Source code |
| makeOncoplot.CPCT | Man page Source code |
| memoSort | Man page Source code |
| performCHORD | Man page Source code |
| performGISTIC2 | Man page Source code |
| performLINX | Man page Source code |
| performShatterSeek | Man page Source code |
| plotMutationalSignaturesCOSMIC | Man page Source code |
| plotMutationalSignaturesCustom | Man page Source code |
| plotOverviewGISTIC2 | Man page Source code |
| proposedAetiologyCOSMICv3.2 | Man page |
| proteinDomains | Man page |
| retrieveDESeq2Results | Man page Source code |
| retrieveFilesWGS | Man page Source code |
| runArriba | Man page Source code |
| rundNdS | Man page Source code |
