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| calFst | calFst |
| calJSI | compareJSI |
| calNeiDist | calNeiDist |
| ccfAUC | ccfAUC |
| classifyMut | classifyMut |
| cna2gene | cna2gene |
| compareCCF | compareCCF |
| compareTree | compareTree |
| fitSignatures | fitSignatures |
| getBinaryMatrix | getBinaryMatrix |
| getBinaryMatrix-method | getBinaryMatrix |
| getBootstrapValue | getBootstrapValue |
| getBootstrapValue-method | getBootstrapValue |
| getBranchType | getBranchType |
| getBranchType-method | getBranchType |
| getCCFMatrix | getCCFMatrix |
| getCCFMatrix-method | getCCFMatrix |
| getMafData | getMafData |
| getMafData-method | getMafData |
| getMafPatient | getMafPatient |
| getMafPatient-method | getMafPatient |
| getMafRef | getMafRef |
| getMafRef-method | getMafRef |
| getMutBranches | getMutBranches |
| getMutBranches-method | getMutBranches |
| getNonSyn_vc | getNonSyn_vc |
| getNonSyn_vc-method | getNonSyn_vc |
| getPhyloTree | getPhyloTree |
| getPhyloTreePatient | getPhyloTreePatient |
| getPhyloTreePatient-method | getPhyloTreePatient |
| getPhyloTreeRef | getPhyloTreeRef |
| getPhyloTreeRef-method | getPhyloTreeRef |
| getPhyloTreeTsbLabel | getPhyloTreeRef |
| getPhyloTreeTsbLabel-method | getPhyloTreeRef |
| getSampleInfo | getSampleInfo |
| getSampleInfo-method | getSampleInfo |
| getTree | getTree |
| getTree-method | getTree |
| getTreeMethod | getTreeMethod |
| getTreeMethod-method | getTreeMethod |
| Maf | Maf class |
| Maf-class | Maf class |
| MafList | MafList class |
| MafList-class | MafList class |
| mathScore | mathScore |
| mutCluster | mutCluster |
| mutHeatmap | mutHeatmap |
| mutTrunkBranch | mutTrunkBranch |
| phyloTree | phyloTree class |
| phyloTree-class | phyloTree class |
| phyloTreeList-class | phyloTreeList class |
| plotCNA | plotCNA |
| plotMutProfile | plotMutProfile |
| plotMutSigProfile | plotMutSigProfile |
| plotPhyloTree | plotPhyloTree |
| readMaf | readMaf |
| readSegment | readSegment |
| runMesKit | Run the default MesKit app for analysis locally |
| subMaf | Subset Maf object |
| testNeutral | testNeutral |
| triMatrix | triMatrix |