├── COPYING ├── DESCRIPTION ├── LogoSCEVAN.png ├── MGH106_annot.png ├── NAMESPACE ├── R ├── CNcall.R ├── classifyTumor.R ├── confidentNormal.R ├── createHTML.R ├── getGenes.R ├── multiSampleComparisonClonalCN.R ├── mwwFunc.R ├── pipelineCNA.R ├── plotHeatmap.R ├── plotSegmentation.R ├── preProcessing.R ├── qvalue.R ├── sortData.R ├── sysdata.rda ├── testFunc.R └── vegaMC.R ├── README.md ├── SCEVAN_workflow.png ├── man ├── SCEVAN.Rd ├── annotateGenes.Rd ├── annoteBandOncoHeat.Rd ├── classifyCluster.Rd ├── classifyTumorCells.Rd ├── computeCNAmtx.Rd ├── getBreaksVegaMC.Rd ├── getConfidentNormalCells.Rd ├── multiSampleComparisonClonalCN.Rd ├── pipelineCNA.Rd ├── plotAllClonalCN.Rd ├── plotAllSubclonalCN.Rd ├── plotCNA_withAnnotCells.Rd ├── removeSyntheticBaseline.Rd ├── sortData.Rd └── top30classification.Rd ├── src ├── run_vegaMC.c ├── run_vegaMC.o ├── sort_data.o ├── vegaMC.c └── vegaMC.o └── vignettes ├── .gitignore ├── IntratumoralHeterogeneityInGlioblastoma.Rmd ├── 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