API for waldronlab/subtypeHeterogeneity
Tumor subclonality of expression-based cancer subtypes
| Global functions | |
|---|---|
| .clusterCalls | Source code |
| .decideCellType | Source code |
| .extractLower | Source code |
| .extractUpper | Source code |
| .getMergeIndex | Source code |
| .getROHits | Source code |
| .getStateColors | Source code |
| .getStateLegend | Source code |
| .isSubClonal | Source code |
| .maxScore | Source code |
| .pruneMultiAssign | Source code |
| .readAbsolute | Source code |
| .readPurityPloidy | Source code |
| .totalCN | Source code |
| .wmean | Source code |
| analyzeCancerType | Source code |
| analyzeCooccurence | Source code |
| analyzeStrata | Source code |
| annoCellType | Source code |
| annotateCytoBands | Source code |
| bpCrossType | Source code |
| bpCyclins | Source code |
| bpSubtypeStrata | Source code |
| bpType | Source code |
| circosSubtypeAssociation | Source code |
| compileMarkers | Source code |
| corPermTest | Source code |
| extendObservations | Source code |
| facetTumors | Source code |
| generateInferCNVInput | Source code |
| getAmbigiousCalls | Source code |
| getBroadSubtypes | Source code |
| getCellAnnotation | Source code |
| getCelltypeSubtypeMatrix | Source code |
| getClassProbs | Source code |
| getClassifierGenes | Source code |
| getCnvGenesFromTCGA | Source code |
| getCommonMarkers | Source code |
| getExtendedVerhaakSignature | Source code |
| getGISTIC | Source code |
| getMatchedAbsoluteCalls | Source code |
| getPerc | Source code |
| getRecurrentDriverGenes | Source code |
| ggplotSubtypeStrata | Source code |
| gistic2RSE | Source code |
| mapOVSubtypes | Source code |
| margin | Source code |
| markerHeatmap | Source code |
| markerHeatmapList | Source code |
| matrixPlot | Source code |
| plotCommonSCNAs | Source code |
| plotCorrelation | Source code |
| plotMainCellTypes | Source code |
| plotNrCNAsPerSubtype | Source code |
| plotNrSamples | Source code |
| plotNrSubtypesVsNrGisticRegions | Source code |
| plotPurityStrata | Source code |
| plotSubclonalityDistributions | Source code |
| plotSubtypePurityPloidy | Source code |
| plotType | Source code |
| plotlyPie | Source code |
| populationRanges | Source code |
| populationRangesRO | Source code |
| preprocessSCE | Source code |
| pseudotimeHeatmap | Source code |
| querySubclonality | Source code |
| readObservations | Source code |
| scHeatmap | Source code |
| scHeatmap2 | Source code |
| stratifyByPurity | Source code |
| stratifySubclonality | Source code |
| subsetByCellType | Source code |
| subsetObservations | Source code |
| symbols2ranges | Source code |
| testSubtypes | Source code |
| tissueScore | Source code |
| transferCellType | Source code |
| volcanoCorrelation | Source code |
