Nik-Zainal-Group/signature.tools.lib
signature.tools.lib

Package index
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Vignettes
Functions
325
Source code
72
Man pages
100
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Nik-Zainal-Group/signature.tools.lib: signature.tools.lib
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API

API for Nik-Zainal-Group/signature.tools.lib
signature.tools.lib

Global functions
Fit Man page Source code
FitMS Man page Source code
HRDetect_pipeline Man page Source code
KLD Man page Source code
MAD Source code
NMAD 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
assignSignatureProbabilityToMutations Man page Source code
average_medoids_cosSim Source code
bedpeToRearrCatalogue Man page Source code
biasCountsToOddRatios Source code
biasCountsToProportions Source code
biasCountsToRatios Source code
bleedingFilter Source code
bleedingFilterKLD Source code
build_junctions_catalogue Source code
calc.ai Man page Source code
calc.hrd Man page Source code
calc.lst Man page Source code
cataloguesClustering Man page Source code
check.names.fn Source code
classifyRearrangementsFromBedpe Source code
combineDNVtables Source code
combinePerformanceExposures Source code
combineStrandBiasResults Man page Source code
compact Source code Source code
compareError Source code
computeCorrelation Source code
computeCorrelationOfTwoSetsOfSigs Man page Source code
computeCorrelation_parallel Man page Source code
computePropTooSimilar Source code
convertDNVchannelFromZouToAlexandrov Source code
convertExposuresFromOrganToRefSigs Man page Source code
convertExposuresFromOrganToRefSigsIfAny Man page Source code
convertSigNamesFromOrganToRefSigs Source code
convertSigNamesFromOrganToRefSigs_subroutine Source code
convertToAlexandrovChannels Man page Source code
cos_sim Man page Source code
dnvTabToDNVcatalogue Man page Source code
dnvTabToTNVcatalogue Man page Source code
drawCircle Source code
evaluatePerformanceExposures Man page Source code
evaluatePerformanceExposuresCore Source code
evaluatePerformanceExposuresList Man page Source code
evaluatePerformanceSignatureSimilarity Man page Source code
evaluatePerformanceSignatureSimilarityList Man page Source code
exactPcf Source code
expandColumnToMatrix Man page Source code
export_SignatureFit_withBootstrap_to_JSON Man page Source code
exposureDistributionBarplot Man page Source code
filterMarkS4 Source code
finalcaller Source code
finaliseCommonRareSignatureExposures Man page 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
findContextSNV Man page Source code
findEst Source code
findKataegis Man page Source code
findMarks Source code
findMedoidsHclust Source code
findsmallestrep Source code
fitMStoJSON Man page Source code
fitMerge Man page Source code
fitSignaturesAndSave Source code
fitSignaturesWithSignatures Man page Source code
fitToJSON Man page Source code
flexconstr_sigfit Source code
flexconstr_sigfit_multipleSamples Source code
flip Source code
fromVcfToTable Source code
generateHist Source code
generateRandMuts Source code
genomeChart Man page Source code
genomeChartSV Man page Source code
genomePlot Man page Source code
getArcCoordinates Source code
getCNColoursAndRanges Source code
getCOSMICSignatures Man page Source code
getClustersColours Source code
getGiniThresholds Man page Source code
getIndelsClassColours Source code
getKellyColours Source code
getMad Source code
getMutTables Source code
getMutTablesTab Source code
getOrganSignatures Man page Source code
getReferenceSignatures Man page Source code
getSBSCatalogueColours Source code
getSBScataloguesInSVclusters Source code
getSVClassColours Source code
getSVClassColours_SVCatalogue Source code
getSVinRange Source code
getSignaturesForFitting Man page Source code
getTypeOfMutationsFromChannels Source code
get_all_factors Source code
giniCoeff Source code
hotspotInfo Source code
indelsToCountAndProportion Source code
loadFitFromFile Man page Source code
loadSimulatedData Man page 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
mutToBases Source code
mutationSampling Man page Source code
no.tel Source code
normaliseSamples Source code
objSimAnnelaingFunction Source code
oddRatio Man page Source code
partialNMFresidual Source code
plotCNVlegend Source code
plotCircos Source code
plotCircosSV Source code
plotClustersLegend Source code
plotContextSNV Man page Source code
plotCopyNumbers Man page Source code
plotCosSimSignatures Man page Source code
plotDNVSignatures Man page Source code
plotDNVSignaturesCompact Man page Source code
plotDNVSignatures_withMeanSd Source code
plotExposures Source code
plotFit Man page Source code
plotFitMS Man page Source code
plotFitResults Man page Source code
plotGenericSignatures Man page Source code
plotGenericSignatures_withMeanSd Source code
plotHierarchicalCluster Source code
plotIndelsClassSummary Source code
plotJunctionsCatalogues Man page Source code
plotMatrix Man page Source code
plotMessage Source code
plotOverallMetrics Source code
plotPerformanceExposures Source code
plotPerformanceSignatures Source code
plotPerformanceSignaturesList Source code
plotRearrSignatures Man page Source code
plotRearrSignatures_withMeanSd Source code
plotRegion Man page Source code
plotSignatures Man page Source code
plotStrandBiasResults Man page Source code
plotSubsSignatures Man page Source code
plotSubsSignaturesCompact Man page Source code
plotSubsSignatures_withMeanSd Source code
plotTNVcatalogues Man page 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
polarToCartesian 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
rareSignatureExtraction Man page 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
sampleStrandBias Man page Source code
saveFitToFile Man page Source code
saveSimulatedData Man page Source code
selectFastPcf Source code
set.plot.params Source code
shrink.seg Source code
shrink.seg.ai Source code
signatureFit_pipeline Man page Source code
simpleBarChart Source code
simpleBoxPlot Source code
simpleCatalogueSimulation Man page Source code
slice_cnv_table_to_regions Source code
slice_sv_table_to_regions Source code
snvTabToDNVcatalogue Man page Source code
sortCatalogue Man page Source code
startSolution Source code
subs_clustering Source code
tabToDNVcatalogue Man page Source code
tabToIndelsClassification Man page Source code
tabToSNVcatalogue Man page Source code
tableToJSON Source code
tandemcount Source code
tnvTabToTNVcatalogue Man page Source code
toPyr Source code
toPyrMutation Source code
unexplainedSamples Man page Source code
updateDataMatrix Source code
updateSigNamesWithMatchTable Man page Source code
vcfToDNVcatalogue Man page Source code
vcfToIndelsClassification Man page Source code
vcfToSNVcatalogue Man page Source code
vectorToJSON Source code
withinClusterCosSim Source code
writeFitResultsToJSON Man page Source code
writeTable Man page Source code
Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.

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