Files in J0bbie/R2CPCT
Misc. functions to perform import and analysis of WGS and RNA-Seq samples
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/analysisRNA_retrieveDESeq2Results.R
R/analysisRNA_runArriba.R
R/analysisWGS_detectEnrichmentOfMutants.R
R/analysisWGS_detectKataegis_Old.R
R/analysisWGS_determineMutationalBurden.R
R/analysisWGS_determineTiTv.R
R/analysisWGS_fitCustomMutSigs.R
R/analysisWGS_fitMutSigs.R
R/analysisWGS_generateCombinedReport.R
R/analysisWGS_rundNdS.R
R/data.R
R/helper_importWGSOfSample.R
R/import_LINXFusions.R
R/import_driverCatalogHMF.R
R/import_importGISTIC2.R
R/import_performCHORD.R
R/import_performGISTIC2.R
R/import_performLINX.R
R/import_performShatterSeek.R
R/import_purityStatsPURPLE.R
R/import_retrieveFilesWGS.R
R/import_somaticCopynumbersPURPLE.R
R/import_somaticStructuralVariantsPURPLE.R
R/import_somaticVariantsVEP.R
R/misc_cleanSeqLevels.R
R/misc_findCPCTCenter.R
R/misc_initializeLogger.R
R/misc_memoSort.R
R/plot_MutationalSignaturesCOSMIC.R
R/plot_MutationalSignaturesCustom.R
R/plot_oncoplot.R
R/plot_overviewGISTIC2.R
README.md
data/GENCODE.v38.Exons.rda
data/GENCODE.v38.rda
data/driverList.rda
data/proposedAetiologyCOSMICv3.2.rda
data/proteinDomains.rda
inst/extdata/CPCTSites.txt
inst/extdata/largeGenes_FLAGS.txt
inst/extdata/refCDS_ENSEMBLv104_HMF.rda
man/GENCODE.v38.Exons.Rd
man/GENCODE.v38.Rd
man/cleanSeqlevels.Rd
man/detectEnrichmentOfMutants.Rd
man/detectKataegis_OLD.Rd
man/determineMutationalBurden.Rd
man/determineTiTv.Rd
man/driverList.Rd
man/findCPCTCenter.Rd
man/fitCustomMutSigs.Rd
man/fitMutSigs.Rd
man/generateCombinedReport.Rd
man/importArriba.Rd
man/importGISTIC2.Rd
man/importLINXFusions.Rd
man/importPurityStatsPURPLE.Rd
man/importSomaticCopynumberPURPLE.Rd
man/importSomaticVariantsVEP.Rd
man/importStructuralVariantsPURPLE.Rd
man/importWGSOfCohort.Rd
man/importWGSOfSample.Rd
man/importdriverCatalogHMF.Rd
man/initializeLogger.Rd
man/makeOncoplot.CPCT.Rd
man/memoSort.Rd
man/performCHORD.Rd
man/performGISTIC2.Rd
man/performLINX.Rd
man/performShatterSeek.Rd
man/plotMutationalSignaturesCOSMIC.Rd
man/plotMutationalSignaturesCustom.Rd
man/plotOverviewGISTIC2.Rd
man/proposedAetiologyCOSMICv3.2.Rd
man/proteinDomains.Rd
man/retrieveDESeq2Results.Rd
man/retrieveFilesWGS.Rd
man/runArriba.Rd
man/rundNdS.Rd
misc/generateDriverList.R
vignettes/globalMethodology.rmd
vignettes/howToInstallLINX.rmd
