API for KarchinLab/pictograph
Tools for modeling clonal evolution of a cancer
| Global functions | |
|---|---|
| allThreshes | Man page Source code |
| assignMultiplicity | Source code |
| bfsLong2 | Source code |
| bridgeTestBFS | Source code |
| calcChainBIC | Source code |
| calcConstrianedTreeSpace | Source code |
| calcSubcloneProportions | Man page Source code |
| calcTreeScores | Man page |
| calcmC | Source code |
| calculateTreeScoreMutations | Man page |
| checkEdge | Source code |
| collectBestKChains | Man page |
| colorScheme | Man page Source code |
| constrainedEdges | Source code |
| constrainedEdgesMatrix | Source code |
| enumerateSpanningTreesModified | Man page Source code |
| estimateClusterAssignments | Man page |
| estimateICN | Man page Source code |
| estimateMCFs | Man page Source code |
| estimateMultiplicity | Man page Source code |
| estimateMultiplicity1 | Source code |
| estimateMultiplicityMatrix | Source code |
| filterEdgesBasedOnCCFs | Man page Source code |
| filterK | Source code |
| formatChains | Source code |
| generateAllTrees | Man page Source code |
| generateTiers | Source code |
| generateZPostSummary | Source code |
| get.parameter.chain | Source code |
| get95CI | Source code |
| getAllNodes | Source code |
| getBoxInputData | Source code |
| getmCCI | Source code |
| growModified | Source code |
| importFiles | Man page Source code |
| importMutationFileOnly | Man page Source code |
| matchSamplePresence | Source code |
| mcmcMain | Man page Source code |
| mergeSetChains | Man page |
| numberClusters | Source code |
| numberSamples | Source code |
| pictograph | Man page |
| pictograph-package | Man page |
| plotAllTrees | Man page Source code |
| plotChainsMCF | Man page Source code |
| plotClusterAssignmentProbVertical | Man page Source code |
| plotEnsembleTree | Man page Source code |
| plotGraph | Source code |
| plotMCFViolin | Man page Source code |
| plotPosteriorAmLong | Source code |
| plotSubcloneBar | Man page |
| plotSubclonePie | Man page Source code |
| plotTree | Man page Source code |
| plotViolin | Source code |
| pop | Source code |
| prepareGraph | Man page Source code |
| reverseDrop | Source code |
| reversedConnection | Source code |
| runMCMC | Source code |
| runMCMCForABox | Source code |
| runMCMCForAllBoxes | Man page Source code |
| runMutSetMCMC | Source code |
| satisfiesSumCondition | Source code |
| separateMutationsBySamplePresence | Man page Source code |
| simulation | Source code |
| simulation_CNA_germline_SNV | Source code |
| simulation_normal | Source code |
| simulation_type1_jags | Source code |
| simulation_type2_jags | Source code |
| simulation_type3_jags | Source code |
| summarizeZPost | Source code |
| verticesInGraph | Source code |
| violinProcessData | Source code |
| writeClusterAssignmentsTable | Man page |
| writeClusterMCFsTable | Man page Source code |
| writeIcnTable | Man page Source code |
| writeMultiplicityTable | Man page Source code |
| writeSetKTable | Man page |
