API for pdiakumis/hrdetect
Signature Tools
| Global functions | |
|---|---|
| HRDetect_pipeline | Man page Source code |
| KLD | Man page Source code |
| PottsCompact | Source code |
| RMSE | Man page Source code |
| SignatureExtraction | Man page Source code |
| SignatureFit | Man page Source code |
| SignatureFit_withBootstrap | Man page Source code |
| SignatureFit_withBootstrap_Analysis | Man page Source code |
| applyHRDetectDavies2017 | Man page Source code |
| ascatToHRDLOH | Man page Source code |
| assignPvalues | Source code |
| average_medoids_cosSim | Source code |
| bedpeToRearrCatalogue | Man page Source code |
| bleedingFilter | Source code |
| bleedingFilterKLD | Source code |
| calc.ai | Man page Source code |
| calc.hrd | Man page Source code |
| calc.lst | Man page Source code |
| check.names.fn | Source code |
| classifyRearrangementsFromBedpe | Source code |
| compact | Source code Source code |
| computeCorrelation | Source code |
| computeCorrelationOfTwoSetsOfSigs | Man page Source code |
| computeCorrelation_parallel | Source code |
| computePropTooSimilar | Source code |
| cos.sim | Man page Source code |
| exactPcf | Source code |
| export_SignatureFit_withBootstrap_to_JSON | Man page Source code |
| exposureDistributionBarplot | Man page Source code |
| filterMarkS4 | Source code |
| finalcaller | Source code |
| findClosestCOSMIC30 | Man page Source code |
| findClosestCOSMIC30_withSimilarity | Man page Source code |
| findClosestCOSMIC30andCombinations | Man page Source code |
| findClosestCOSMIC30andCombinations_withSimilarity | Man page Source code |
| findClosestRearrSigsBreast560 | Source code |
| findClosestRearrSigsBreast560_withSimilarity | Source code |
| findEst | Source code |
| findMarks | Source code |
| findMedoidsHclust | Source code |
| findsmallestrep | Source code |
| generateHist | Source code |
| generateRandMuts | Source code |
| genomePlot | Man page Source code |
| getMad | Source code |
| getMutTables | Source code |
| getMutTablesTab | Source code |
| get_all_factors | Source code |
| hotspotInfo | Source code |
| indelsToCountAndProportion | Source code |
| markWithPotts | Source code |
| matchRuns | Source code |
| matchedClustering | Man page Source code |
| maxBetweenClustersCosSim | Source code |
| maxMatchRuns | Source code |
| medianFilter | Source code |
| medoids_cosSimMatrix | Source code |
| merge.with.order | Source code Source code |
| mh | Source code |
| mhcaller | Source code |
| minWithinClusterCosSim | Source code |
| no.tel | Source code |
| normaliseSamples | Source code |
| objSimAnnelaingFunction | Source code |
| plot.CosSimMatrix | Source code |
| plot.CosSimSignatures | Man page Source code |
| plot.exposures | Source code |
| plotGenericSignatures | Man page Source code |
| plotGenericSignatures_withMeanSd | Source code |
| plotHierarchicalCluster | Source code |
| plotOverallMetrics | Source code |
| plotRearrSignatures | Man page Source code |
| plotRearrSignatures_withMeanSd | Source code |
| plotSubsSignatures | Man page Source code |
| plotSubsSignatures_withMeanSd | Source code |
| plotWithinClusterCosSim | Source code |
| plotWithinClusterSilWidth | Source code |
| plot_HRDLOH_HRDetect_Contributions | Man page Source code |
| plot_HRDetect_BootstrapScores | Man page Source code |
| plot_HRDetect_Contributions | Man page Source code |
| plot_HRDetect_overall | Man page Source code |
| plot_SignatureFit_withBootstrap | Man page Source code |
| prepare.indel.df | Source code |
| prepare.indel.df_tabversion | Source code |
| prepare.rearr.catalogue_fromAnnotatedBedpe | Source code |
| preprocessCatalgue | Source code |
| processSubs | Source code |
| read.ascat | Source code |
| read.brass.bedpe | Source code |
| read.brassII | Source code Source code |
| readTable | Man page Source code |
| rearrangement.clustering_bedpe | Source code |
| removeSimilarCatalogueSamples | Source code |
| repcaller | Source code |
| runFastPcf | Source code |
| runPcfSubset | Source code |
| selectFastPcf | Source code |
| set.plot.params | Source code |
| shadowtext | Source code |
| shrink.seg | Source code |
| shrink.seg.ai | Source code |
| sortCatalogue | Man page Source code |
| startSolution | Source code |
| tabToIndelsClassification | Man page Source code |
| tabToSNVcatalogue | Man page Source code |
| tandemcount | Source code |
| toPyr | Source code |
| unexplainedSamples | Man page Source code |
| vcfToIndelsClassification | Man page Source code |
| vcfToSNVcatalogue | Man page Source code |
| withinClusterCosSim | Source code |
| writeTable | Man page Source code |
