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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(Fit)
export(FitMS)
export(HRDetect_pipeline)
export(KLD)
export(RMSE)
export(SignatureExtraction)
export(SignatureFit)
export(SignatureFit_withBootstrap)
export(SignatureFit_withBootstrap_Analysis)
export(applyHRDetectDavies2017)
export(ascatToHRDLOH)
export(assignSignatureProbabilityToMutations)
export(bedpeToRearrCatalogue)
export(calc.ai)
export(calc.hrd)
export(calc.lst)
export(cataloguesClustering)
export(combineStrandBiasResults)
export(computeCorrelationOfTwoSetsOfSigs)
export(computeCorrelation_parallel)
export(convertExposuresFromOrganToRefSigs)
export(convertExposuresFromOrganToRefSigsIfAny)
export(convertToAlexandrovChannels)
export(cos_sim)
export(dnvTabToDNVcatalogue)
export(dnvTabToTNVcatalogue)
export(evaluatePerformanceExposures)
export(evaluatePerformanceExposuresList)
export(evaluatePerformanceSignatureSimilarity)
export(evaluatePerformanceSignatureSimilarityList)
export(expandColumnToMatrix)
export(export_SignatureFit_withBootstrap_to_JSON)
export(exposureDistributionBarplot)
export(finaliseCommonRareSignatureExposures)
export(findClosestCOSMIC30)
export(findClosestCOSMIC30_withSimilarity)
export(findClosestCOSMIC30andCombinations)
export(findClosestCOSMIC30andCombinations_withSimilarity)
export(findKataegis)
export(fitMStoJSON)
export(fitMerge)
export(fitSignaturesWithSignatures)
export(fitToJSON)
export(genomeChart)
export(genomeChartSV)
export(genomePlot)
export(getCOSMICSignatures)
export(getGiniThresholds)
export(getOrganSignatures)
export(getReferenceSignatures)
export(getSignaturesForFitting)
export(giniCoeff)
export(loadFitFromFile)
export(loadSimulatedData)
export(matchedClustering)
export(mutationSampling)
export(oddRatio)
export(plotCopyNumbers)
export(plotCosSimSignatures)
export(plotDNVSignatures)
export(plotDNVSignaturesCompact)
export(plotExposures)
export(plotFit)
export(plotFitMS)
export(plotFitResults)
export(plotGenericSignatures)
export(plotJunctionsCatalogues)
export(plotMatrix)
export(plotRearrSignatures)
export(plotSignatures)
export(plotStrandBiasResults)
export(plotSubsSignatures)
export(plotSubsSignaturesCompact)
export(plotTNVcatalogues)
export(plot_HRDLOH_HRDetect_Contributions)
export(plot_HRDetect_BootstrapScores)
export(plot_HRDetect_Contributions)
export(plot_HRDetect_overall)
export(plot_SignatureFit_withBootstrap)
export(rareSignatureExtraction)
export(readTable)
export(sampleStrandBias)
export(saveFitToFile)
export(saveSimulatedData)
export(signatureFit_pipeline)
export(simpleCatalogueSimulation)
export(snvTabToDNVcatalogue)
export(sortCatalogue)
export(tabToDNVcatalogue)
export(tabToIndelsClassification)
export(tabToSNVcatalogue)
export(tnvTabToTNVcatalogue)
export(unexplainedSamples)
export(updateSigNamesWithMatchTable)
export(vcfToDNVcatalogue)
export(vcfToIndelsClassification)
export(vcfToSNVcatalogue)
export(writeFitResultsToJSON)
export(writeTable)
importFrom(foreach,"%dopar%")