API for PoisonAlien/maftools
Summarize, Analyze and Visualize MAF Files
| Global functions | |
|---|---|
| GISTIC | Man page |
| GISTIC-class | Man page |
| MAF | Man page |
| MAF-class | Man page |
| add_legend | Source code |
| add_oncoprint | Source code |
| add_oncoprint2 | Source code |
| annovarToMaf | Man page Source code |
| clinicalEnrichment | Man page Source code |
| cluster_prot | Source code |
| coOncoplot | Man page Source code |
| createOncoMatrix | Source code |
| dashboard | Source code |
| detectCP | Source code |
| dirichletClusters | Source code |
| extractSignatures | Man page Source code |
| filterCopyNumber | Source code |
| fisherCorrection | Source code |
| forestPlot | Man page Source code |
| geneCloud | Man page Source code |
| genesToBarcodes | Man page Source code |
| genotypeMatrix | Man page Source code |
| getClinicalData | Man page Man page |
| getClinicalData,MAF-method | Man page |
| getCytobandSummary | Man page Man page |
| getCytobandSummary,GISTIC-method | Man page |
| getFields | Man page Man page |
| getFields,MAF-method | Man page |
| getGeneSummary | Man page Man page Man page |
| getGeneSummary,GISTIC-method | Man page |
| getGeneSummary,MAF-method | Man page |
| getOncoPlot | Source code |
| getSampleSummary | Man page Man page Man page |
| getSampleSummary,GISTIC-method | Man page |
| getSampleSummary,MAF-method | Man page |
| get_lp_data | Source code |
| get_threshold | Source code |
| get_titvCol | Source code |
| get_vcColors | Source code |
| gisticBubblePlot | Man page Source code |
| gisticChromPlot | Man page Source code |
| gisticMap | Source code |
| gisticOncoPlot | Man page Source code |
| icgcSimpleMutationToMAF | Man page Source code |
| inferHeterogeneity | Man page Source code |
| label_pos | Source code |
| lollipopPlot | Man page Source code |
| lollipopPlot2 | Man page Source code |
| mafCompare | Man page Source code |
| mafSummary | Man page Source code |
| mafSurvival | Man page Source code |
| mapMutsToSegs | Source code |
| math.score | Man page Source code |
| mutCountMatrix | Man page Source code |
| oncodrive | Man page Source code |
| oncoplot | Man page Source code |
| oncostrip | Man page Source code |
| oncotate | Man page Source code |
| pancanComparison | Man page Source code |
| parse_prot | Source code |
| pfamDomains | Man page Source code |
| plotApobecDiff | Man page Source code |
| plotCBS | Source code |
| plotCBSchr | Source code |
| plotCBSsegments | Man page Source code |
| plotClusters | Man page Source code |
| plotEnrichmentResults | Man page Source code |
| plotOncodrive | Man page Source code |
| plotSignatures | Man page Source code |
| plotTiTv | Man page Source code |
| plotVaf | Man page Source code |
| plotmafSummary | Man page Source code |
| prepareMutSig | Man page Source code |
| rainfallPlot | Man page Source code |
| read.maf | Man page Source code |
| readGistic | Man page Source code |
| readSegs | Source code |
| refineClusters | Source code |
| repelPoints | Source code |
| shiftPoints | Source code |
| signatureEnrichment | Man page Source code |
| somaticInteractions | Man page Source code |
| sortByAnnotation | Source code |
| sortByGeneOrder | Source code |
| sortByMutation | Source code |
| sortByMutationKeepGeneOrder | Source code |
| subsetMaf | Man page Source code |
| summarizeGistic | Source code |
| summarizeMaf | Source code |
| tcgaCompare | Man page Source code |
| titv | Man page Source code |
| transformSegments | Source code |
| trinucleotideMatrix | Man page Source code |
| validateMaf | Source code |
| write.GisticSummary | Man page Source code |
| write.mafSummary | Man page Source code |
