Files in pdiakumis/hrdetect
Signature Tools
.Rbuildignore
.gitignore
DESCRIPTION
LICENCE
NAMESPACE
R/Functions.GenomicScars.R
R/HRDetect.R
R/RCircos_utils.R
R/SignatureExtractionLib.R
R/SignatureFitLib.R
R/ascatToHRDLOH.R
R/bedpeToRearrCatalogue.R
R/catalogue_building_utils.R
R/fastPCF.R
R/genomePlot.R
R/genomePlot_utils.R
R/matchedClustering.R
R/microhomology.R
R/signatures_utils.R
R/sysdata.rda
R/tabToIndelsClassification.R
R/tabToSNVcatalogue.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/chrominfo.RData
data/chrominfo.snp6.hg19.RData
data/karyotype.dog.txt
examples/Example01/Example01.R
examples/Example01/expectedOutput/HRDetect_res_expectedOutput.tsv
examples/Example01/expectedOutput/SNV_catalogues_expectedOutput.jpg
examples/Example01/expectedOutput/signatureFit_expectedOutput/SigFit_withBootstrap_Exposures_mKLD_bfmCosSim_alpha-1_tr5_p0.05.jpg
examples/Example01/expectedOutput/signatureFit_expectedOutput/SigFit_withBootstrap_Exposures_mKLD_bfmCosSim_alpha-1_tr5_p0.05.tsv
examples/Example01/expectedOutput/signatureFit_expectedOutput/SigFit_withBootstrap_Summary_mKLD_bfmCosSim_alpha-1_tr5_p0.05.rData
examples/Example01/expectedOutput/signatureFit_expectedOutput/SigFit_withBootstrap_Summary_mKLD_bfmCosSim_alpha-1_tr5_p0.05/sigfit_bootstrap_1of2.jpg
examples/Example01/expectedOutput/signatureFit_expectedOutput/SigFit_withBootstrap_Summary_mKLD_bfmCosSim_alpha-1_tr5_p0.05/sigfit_bootstrap_2of2.jpg
man/.Rapp.history
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/bedpeToRearrCatalogue.Rd
man/calc.ai.Rd
man/calc.hrd.Rd
man/calc.lst.Rd
man/computeCorrelationOfTwoSetsOfSigs.Rd
man/cos.sim.Rd
man/export_SignatureFit_withBootstrap_to_JSON.Rd
man/exposureDistributionBarplot.Rd
man/findClosestCOSMIC30.Rd
man/findClosestCOSMIC30_withSimilarity.Rd
man/findClosestCOSMIC30andCombinations.Rd
man/findClosestCOSMIC30andCombinations_withSimilarity.Rd
man/genomePlot.Rd
man/matchedClustering.Rd
man/plot.CosSimSignatures.Rd
man/plotGenericSignatures.Rd
man/plotRearrSignatures.Rd
man/plotSubsSignatures.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/readTable.Rd
man/sortCatalogue.Rd
man/tabToIndelsClassification.Rd
man/tabToSNVcatalogue.Rd
man/unexplainedSamples.Rd
man/vcfToIndelsClassification.Rd
man/vcfToSNVcatalogue.Rd
man/writeTable.Rd
scripts/README.md
scripts/hrDetect.R
signature.tools.lib.Rproj
signature.tools.lib.develop.R
tests/testthat/HRDetect_data_table.test.tsv
tests/testthat/ascat_test.csv
tests/testthat/genomePlot.test.png
tests/testthat/hrdetect_output_example.tsv
tests/testthat/test-HRDetect.R
tests/testthat/test-SignatureExtraction.R
tests/testthat/test-SignatureFit.R
tests/testthat/test-ascatToHRDLOH.R
tests/testthat/test-bedpeToRearrCatalogue.R
tests/testthat/test-genomePlot.R
tests/testthat/test-matchClustering.R
tests/testthat/test-tabToIndelsClassification.R
tests/testthat/test-tabToSNVcatalogue.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.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_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
