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

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signature.tools.lib

.Rbuildignore
.github/workflows/traffic_action.yml
.gitignore
.gitlab-ci.yml
DESCRIPTION
Dockerfile
LICENCE
NAMESPACE
R/DinucleotideVariantsLib.R R/Functions.GenomicScars.R R/HRDetect.R R/RCircos_utils.R R/SignatureExtractionLib.R R/SignatureFitLib.R R/TrinucleotideVariantsLib.R R/ascatToHRDLOH.R R/assignMutationsSignatureProbability.R R/bedpeToRearrCatalogue.R R/catalogue_building_utils.R R/cataloguesClustering.R R/fastPCF.R R/findKataegis.R R/genomeChart.R R/genomeChartSV.R R/genomePlot.R R/genomePlot_utils.R R/matchedClustering.R R/microhomology.R R/mutationContext.R R/performanceEvaluationLib.R R/plotCopyNumbers.R R/plotJunctionsCatalogues.R R/plotRegion.R R/plotSignaturesCompact.R R/rareSignaturesExtractionLib.R R/signatureFitMultiStepLib.R R/signatureFit_pipeline.R R/signatureIdentificationLib.R R/signatures_utils.R R/simpleCatalogueSimulationLib.R R/strandBiasLib.R
R/sysdata.rda
R/tabToIndelsClassification.R R/tabToSNVcatalogue.R R/unexplainedSamples.R R/vcfToIndelsClassification.R R/vcfToSNVcatalogue.R README.md
data/2019_01_10_ConversionMatrix_rearr.tsv
data/2019_01_10_ConversionMatrix_subs.tsv
data/2019_01_10_all_PCAWG_sigs_rearr.tsv
data/2019_01_10_all_PCAWG_sigs_subs.tsv
data/Breast560_rearrangement.signatures.txt
data/COSMIC30_subs_signatures.txt
data/COSMIC_v3.2_DBS_GRCh37.tsv
data/COSMIC_v3.2_SBS_GRCh37.tsv
data/RefSigDBS_v1.01/OrganSpecificSigs_GEL_DBS_v1.01.tsv
data/RefSigDBS_v1.01/OrganSpecificSigs_Hartwig_DBS_v1.01.tsv
data/RefSigDBS_v1.01/OrganSpecificSigs_ICGC_DBS_v1.01.tsv
data/RefSigDBS_v1.01/RefSig_DBS_conversionMatrix_v1.01.tsv
data/RefSigDBS_v1.01/RefSig_DBS_v1.01.tsv
data/RefSigDBS_v1.01/SigsForFitting_DBS_v1.01.tsv
data/RefSigSBS_v2.03/OrganSpecificSigs_GEL_SBS_v2.03.tsv
data/RefSigSBS_v2.03/OrganSpecificSigs_Hartwig_SBS_v2.03.tsv
data/RefSigSBS_v2.03/OrganSpecificSigs_ICGC_SBS_v2.03.tsv
data/RefSigSBS_v2.03/RefSig_SBS_conversionMatrix_v2.03.tsv
data/RefSigSBS_v2.03/RefSig_SBS_v2.03.tsv
data/RefSigSBS_v2.03/SigsForFitting_SBS_v2.03.tsv
data/RefSigv1_Rearr.tsv
data/RefSigv1_Subs.tsv
data/StrandBiasTable.tsv
data/StrandBiasTable_Counts_Pyr_single.tsv
data/StrandBiasTable_Counts_Pyr_tri.tsv
data/chrominfo.RData
data/chrominfo.snp6.hg19.RData
data/karyotype.dog.txt
examples/Example01/Example01.R
examples/Example01/expectedOutput/HRDetect_res.tsv
examples/Example01/expectedOutput/SNV_catalogues.pdf examples/Example01/expectedOutput/signatureFit/exposures.pdf
examples/Example01/expectedOutput/signatureFit/exposures.tsv
examples/Example01/expectedOutput/signatureFit/exposures_prop.pdf examples/Example01/expectedOutput/signatureFit/samples/signatureFit_1of2_sample1_Bootstrap.pdf examples/Example01/expectedOutput/signatureFit/samples/signatureFit_1of2_sample1_Bootstrap_Correlation.pdf examples/Example01/expectedOutput/signatureFit/samples/signatureFit_1of2_sample1_Bootstrap_CorrelationExamples.pdf examples/Example01/expectedOutput/signatureFit/samples/signatureFit_1of2_sample1_pointEstimate.pdf examples/Example01/expectedOutput/signatureFit/samples/signatureFit_2of2_sample2_Bootstrap.pdf examples/Example01/expectedOutput/signatureFit/samples/signatureFit_2of2_sample2_Bootstrap_Correlation.pdf examples/Example01/expectedOutput/signatureFit/samples/signatureFit_2of2_sample2_Bootstrap_CorrelationExamples.pdf examples/Example01/expectedOutput/signatureFit/samples/signatureFit_2of2_sample2_pointEstimate.pdf examples/Example02/Example02.R
examples/Example02/expectedOutput/RefSigSubsExposures.tsv
examples/Example02/expectedOutput/SNV_catalogues.pdf examples/Example02/expectedOutput/signatureFit/exposures.pdf
examples/Example02/expectedOutput/signatureFit/exposures.tsv
examples/Example02/expectedOutput/signatureFit/exposures_prop.pdf examples/Example02/expectedOutput/signatureFit/samples/signatureFit_1of2_sample1_Bootstrap.pdf examples/Example02/expectedOutput/signatureFit/samples/signatureFit_1of2_sample1_Bootstrap_Correlation.pdf examples/Example02/expectedOutput/signatureFit/samples/signatureFit_1of2_sample1_Bootstrap_CorrelationExamples.pdf examples/Example02/expectedOutput/signatureFit/samples/signatureFit_1of2_sample1_pointEstimate.pdf examples/Example02/expectedOutput/signatureFit/samples/signatureFit_2of2_sample2_Bootstrap.pdf examples/Example02/expectedOutput/signatureFit/samples/signatureFit_2of2_sample2_Bootstrap_Correlation.pdf examples/Example02/expectedOutput/signatureFit/samples/signatureFit_2of2_sample2_Bootstrap_CorrelationExamples.pdf examples/Example02/expectedOutput/signatureFit/samples/signatureFit_2of2_sample2_pointEstimate.pdf examples/Example03/Example03.R
examples/Example03/expectedOutput/FitMSresults.json.zip
examples/Example03/expectedOutput/SNV_catalogues.pdf examples/Example03/expectedOutput/signatureFit/exposures.pdf
examples/Example03/expectedOutput/signatureFit/exposures.tsv
examples/Example03/expectedOutput/signatureFit/exposures_prop.pdf examples/Example03/expectedOutput/signatureFit/selectedSolution_sample1/exposures.pdf
examples/Example03/expectedOutput/signatureFit/selectedSolution_sample1/exposures.tsv
examples/Example03/expectedOutput/signatureFit/selectedSolution_sample1/exposures_prop.pdf examples/Example03/expectedOutput/signatureFit/selectedSolution_sample1/signatureFit_1of1_sample1_Bootstrap.pdf examples/Example03/expectedOutput/signatureFit/selectedSolution_sample1/signatureFit_1of1_sample1_Bootstrap_Correlation.pdf examples/Example03/expectedOutput/signatureFit/selectedSolution_sample1/signatureFit_1of1_sample1_Bootstrap_CorrelationExamples.pdf examples/Example03/expectedOutput/signatureFit/selectedSolution_sample1/signatureFit_1of1_sample1_pointEstimate.pdf examples/Example03/expectedOutput/signatureFit/selectedSolution_sample2/exposures.pdf
examples/Example03/expectedOutput/signatureFit/selectedSolution_sample2/exposures.tsv
examples/Example03/expectedOutput/signatureFit/selectedSolution_sample2/exposures_prop.pdf examples/Example03/expectedOutput/signatureFit/selectedSolution_sample2/signatureFit_1of1_sample2_Bootstrap.pdf examples/Example03/expectedOutput/signatureFit/selectedSolution_sample2/signatureFit_1of1_sample2_Bootstrap_Correlation.pdf examples/Example03/expectedOutput/signatureFit/selectedSolution_sample2/signatureFit_1of1_sample2_Bootstrap_CorrelationExamples.pdf examples/Example03/expectedOutput/signatureFit/selectedSolution_sample2/signatureFit_1of1_sample2_pointEstimate.pdf examples/Example04/Example04.R examples/Example04/expectedOutput/SNV_catalogues.pdf
examples/Example04/expectedOutput/annotated_SNVs.tsv
examples/Example04/expectedOutput/signatureFit/exposures.pdf
examples/Example04/expectedOutput/signatureFit/exposures.tsv
examples/Example04/expectedOutput/signatureFit/exposures_prop.pdf examples/Example04/expectedOutput/signatureFit/selectedSolution_sample1/exposures.pdf
examples/Example04/expectedOutput/signatureFit/selectedSolution_sample1/exposures.tsv
examples/Example04/expectedOutput/signatureFit/selectedSolution_sample1/exposures_prop.pdf examples/Example04/expectedOutput/signatureFit/selectedSolution_sample1/signatureFit_1of1_sample1_pointEstimate.pdf examples/Example04/expectedOutput/signatureFit/selectedSolution_sample2/exposures.pdf
examples/Example04/expectedOutput/signatureFit/selectedSolution_sample2/exposures.tsv
examples/Example04/expectedOutput/signatureFit/selectedSolution_sample2/exposures_prop.pdf examples/Example04/expectedOutput/signatureFit/selectedSolution_sample2/signatureFit_1of1_sample2_pointEstimate.pdf examples/Example05/Example05.R
man/.Rapp.history
man/Fit.Rd man/FitMS.Rd man/HRDetect_pipeline.Rd man/KLD.Rd man/RMSE.Rd man/SignatureExtraction.Rd man/SignatureFit.Rd man/SignatureFit_withBootstrap.Rd man/SignatureFit_withBootstrap_Analysis.Rd man/applyHRDetectDavies2017.Rd man/ascatToHRDLOH.Rd man/assignSignatureProbabilityToMutations.Rd man/bedpeToRearrCatalogue.Rd man/calc.ai.Rd man/calc.hrd.Rd man/calc.lst.Rd man/cataloguesClustering.Rd man/combineStrandBiasResults.Rd man/computeCorrelationOfTwoSetsOfSigs.Rd man/computeCorrelation_parallel.Rd man/convertExposuresFromOrganToRefSigs.Rd man/convertExposuresFromOrganToRefSigsIfAny.Rd man/convertToAlexandrovChannels.Rd man/cos_sim.Rd man/dnvTabToDNVcatalogue.Rd man/dnvTabToTNVcatalogue.Rd man/evaluatePerformanceExposures.Rd man/evaluatePerformanceExposuresList.Rd man/evaluatePerformanceSignatureSimilarity.Rd man/evaluatePerformanceSignatureSimilarityList.Rd man/expandColumnToMatrix.Rd man/export_SignatureFit_withBootstrap_to_JSON.Rd man/exposureDistributionBarplot.Rd man/finaliseCommonRareSignatureExposures.Rd man/findClosestCOSMIC30.Rd man/findClosestCOSMIC30_withSimilarity.Rd man/findClosestCOSMIC30andCombinations.Rd man/findClosestCOSMIC30andCombinations_withSimilarity.Rd man/findContextSNV.Rd man/findKataegis.Rd man/fitMStoJSON.Rd man/fitMerge.Rd man/fitSignaturesWithSignatures.Rd man/fitToJSON.Rd man/genomeChart.Rd man/genomeChartSV.Rd man/genomePlot.Rd man/getCOSMICSignatures.Rd man/getGiniThresholds.Rd man/getOrganSignatures.Rd man/getReferenceSignatures.Rd man/getSignaturesForFitting.Rd man/loadFitFromFile.Rd man/loadSimulatedData.Rd man/matchedClustering.Rd man/mutationSampling.Rd man/oddRatio.Rd man/plotContextSNV.Rd man/plotCopyNumbers.Rd man/plotCosSimSignatures.Rd man/plotDNVSignatures.Rd man/plotDNVSignaturesCompact.Rd man/plotFit.Rd man/plotFitMS.Rd man/plotFitResults.Rd man/plotGenericSignatures.Rd man/plotJunctionsCatalogues.Rd man/plotMatrix.Rd man/plotRearrSignatures.Rd man/plotRegion.Rd man/plotSignatures.Rd man/plotStrandBiasResults.Rd man/plotSubsSignatures.Rd man/plotSubsSignaturesCompact.Rd man/plotTNVcatalogues.Rd man/plot_HRDLOH_HRDetect_Contributions.Rd man/plot_HRDetect_BootstrapScores.Rd man/plot_HRDetect_Contributions.Rd man/plot_HRDetect_overall.Rd man/plot_SignatureFit_withBootstrap.Rd man/rareSignatureExtraction.Rd man/readTable.Rd man/sampleStrandBias.Rd man/saveFitToFile.Rd man/saveSimulatedData.Rd man/signatureFit_pipeline.Rd man/simpleCatalogueSimulation.Rd man/snvTabToDNVcatalogue.Rd man/sortCatalogue.Rd man/tabToDNVcatalogue.Rd man/tabToIndelsClassification.Rd man/tabToSNVcatalogue.Rd man/tnvTabToTNVcatalogue.Rd man/unexplainedSamples.Rd man/updateSigNamesWithMatchTable.Rd man/vcfToDNVcatalogue.Rd man/vcfToIndelsClassification.Rd man/vcfToSNVcatalogue.Rd man/writeFitResultsToJSON.Rd man/writeTable.Rd scripts/README.md
scripts/genomeChart
scripts/hrDetect
scripts/signatureFit
scripts/solutionSelectionForFitMS
signature.tools.lib.Rproj
signature.tools.lib.develop.R
tests/testthat/DNVTNVexample/faff4626-615b-416a-b7a6-9d177dcc94a9_DNV.tsv
tests/testthat/DNVTNVexample/faff4626-615b-416a-b7a6-9d177dcc94a9_DNVcatalogue.tsv
tests/testthat/DNVTNVexample/faff4626-615b-416a-b7a6-9d177dcc94a9_TNV.tsv
tests/testthat/DNVTNVexample/faff4626-615b-416a-b7a6-9d177dcc94a9_TNVcatalogue.tsv
tests/testthat/FitAndFitMStests/FitandFitMStestCatalogues.tsv
tests/testthat/FitAndFitMStests/FitandFitMStestCatalogues_DBS.tsv
tests/testthat/FitAndFitMStests/FitandFitMStestExposures.tsv
tests/testthat/FitAndFitMStests/FitandFitMStestExposures_DBS.tsv
tests/testthat/HRDetect_data_table.test.tsv
tests/testthat/ascat_test.csv
tests/testthat/assignSigProbability/sigsProb_test_hrdetect_1.tsv
tests/testthat/exposures/exposuresExampleOrganSpecificV2.tsv
tests/testthat/genomePlot.test.png
tests/testthat/hrdetect_output_example.tsv
tests/testthat/insilico_sample.bedpe
tests/testthat/rareExtraction/SDExample05/catalogues.tsv
tests/testthat/rareExtraction/SDExample05/exposures.tsv
tests/testthat/rareExtraction/SDExample05/signatures.tsv
tests/testthat/strandBias/mmr1_biasTable.tsv
tests/testthat/strandBias/mmr_muts_1.tsv
tests/testthat/strandBias/mmr_muts_2.tsv
tests/testthat/strandBias/mmr_muts_3.tsv
tests/testthat/test-DNVTNVfunctions.R tests/testthat/test-FitAndFitMS.R tests/testthat/test-FitAndFitMS_DBS.R tests/testthat/test-HRDetect.R tests/testthat/test-JSONexport.R tests/testthat/test-SignatureExtraction.R tests/testthat/test-SignatureFit.R tests/testthat/test-SignatureFit_pipeline.R tests/testthat/test-SignaturePartialExtraction.R tests/testthat/test-ascatToHRDLOH.R tests/testthat/test-assignSignatureProbabilityToMutations.R tests/testthat/test-bedpeToRearrCatalogue.R tests/testthat/test-genomeChart.R tests/testthat/test-genomeChartSV.R tests/testthat/test-genomePlot.R tests/testthat/test-matchClustering.R tests/testthat/test-mutationContext.R tests/testthat/test-organSpecificSignatures.R tests/testthat/test-plotCopyNumbers.R tests/testthat/test-plotRegion.R tests/testthat/test-snvTabToDNVcatalogue.R tests/testthat/test-strandBias.R tests/testthat/test-tabToDNVcatalogue.R tests/testthat/test-tabToIndelsClassification.R tests/testthat/test-tabToSNVcatalogue.R tests/testthat/test-vcfToDNVcatalogue.R tests/testthat/test-vcfToIndelsClassification.R tests/testthat/test-vcfToSNVcatalogue.R
tests/testthat/test.bedpe
tests/testthat/test.cat
tests/testthat/test.cnvs.txt
tests/testthat/test.dnv.expected.tab
tests/testthat/test.dnv.vcf.bgz
tests/testthat/test.dnv.vcf.bgz.tbi
tests/testthat/test.dnv.vcf.expected.tsv
tests/testthat/test.indel.vcf.gz
tests/testthat/test.indel.vcf.gz.tbi
tests/testthat/test.snv.tab
tests/testthat/test.sub.vcf.gz
tests/testthat/test.sub.vcf.gz.tbi
tests/testthat/test.tabindels.tsv
tests/testthat/test2.snv.tab
tests/testthat/test_DNVs.snv.simple.txt
tests/testthat/test_hrdetect_1/test_hrdetect_1.cna.txt
tests/testthat/test_hrdetect_1/test_hrdetect_1.expected_sv_bedpe_from_vcf.txt
tests/testthat/test_hrdetect_1/test_hrdetect_1.indel.vcf.gz
tests/testthat/test_hrdetect_1/test_hrdetect_1.indel.vcf.gz.tbi
tests/testthat/test_hrdetect_1/test_hrdetect_1.snv.simple.txt
tests/testthat/test_hrdetect_1/test_hrdetect_1.sv.bedpe
tests/testthat/test_hrdetect_1/test_hrdetect_1.sv.vcf.gz
tests/testthat/test_hrdetect_1/test_hrdetect_1_expected_rearrcat.txt
tests/testthat/test_hrdetect_2/test_hrdetect_2.cna.txt
tests/testthat/test_hrdetect_2/test_hrdetect_2.indel.vcf.gz
tests/testthat/test_hrdetect_2/test_hrdetect_2.indel.vcf.gz.tbi
tests/testthat/test_hrdetect_2/test_hrdetect_2.snv.simple.txt
tests/testthat/test_hrdetect_2/test_hrdetect_2.sv.bedpe
tests/testthat/test_hrdetect_2/test_hrdetect_2.sv.vcf.gz
userManuals/FitMS_userManual.pdf userManuals/RareSignaturesExtraction_userManual.pdf userManuals/genomeChart_commandLine_userManual.pdf userManuals/hrDetect_commandLine_userManual.pdf userManuals/signatureFit_commandLine_userManual.pdf userManuals/solutionSelectionForFitMS_commandLine_userManual.pdf
Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.

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