Files in WuyangFF95/SynSigRun

Run Mutational Signature Analysis Software Packages Using Mutational Spectra generated by SynSigGen

NEWS.md R/BestSignatureAnalyzerResult.R R/Diff4SynDataSets.R R/GlobalVariables.R R/MapSPToSASignatureNamesInExposure.R R/Miscellaneous.R R/RunMutationalPatterns.R R/RunSignatureAnalyzerAttribution.R R/RunSignatureEstimationAttributionOnly.R R/RunSomaticSignatures.R R/RunSparseSignatures.R R/RunYAPSAAttributionOnly.R R/RundecompTumor2SigAttributionOnly.R R/RundeconstructSigsAttributionOnly.R R/Runhdp.R R/RunmSigActAttributionOnly.R R/Runmaftools.R R/RunmutSignatures.R R/RunmutSpec.R R/Runsigfit.R R/Runsigminer.R R/RunsigneR.R R/Runtcsm.R R/SignatureAnalyzerHyperRun.R R/SignatureAnalyzerInteraction.R R/SynSigRun.R R/data.R README.Rmd README.md data-raw/Alexandrov_2020/Run.PRIMARY.SA.COMPOSITE.exome.subset.R data-raw/Alexandrov_2020/Run.SA.DBS.exome.subset.R data-raw/Alexandrov_2020/Run.SA.ID.exome.subset.R data-raw/Alexandrov_2020/Run.SECONDARY.SA.COMPOSITE.exome.subset.R data-raw/Alexandrov_2020/syn.2.7a.7b.abst/sa.sa.96/1.run.SA.R data-raw/Alexandrov_2020/syn.2.7a.7b.abst/sa.sa.COMPOSITE/3.run.SA.R data-raw/Alexandrov_2020/syn.2.7a.7b.abst/sp.sa.COMPOSITE/4.run.SA.R data-raw/Alexandrov_2020/syn.2.7a.7b.abst/sp.sp/2.run.SA.R data-raw/Alexandrov_2020/syn.2.7a.7b.bladder.and.melanoma/sa.sa.96/1.run.SA.R data-raw/Alexandrov_2020/syn.2.7a.7b.bladder.and.melanoma/sa.sa.COMPOSITE/3.run.SA.R data-raw/Alexandrov_2020/syn.2.7a.7b.bladder.and.melanoma/sp.sa.COMPOSITE/4.run.SA.R data-raw/Alexandrov_2020/syn.2.7a.7b.bladder.and.melanoma/sp.sp/2.run.SA.R data-raw/Alexandrov_2020/syn.30.random.sigs/sa.sa.96/1.run.SA.R data-raw/Alexandrov_2020/syn.30.random.sigs/sa.sa.COMPOSITE/3.run.SA.R data-raw/Alexandrov_2020/syn.30.random.sigs/sp.sa.COMPOSITE/4.run.SA.R data-raw/Alexandrov_2020/syn.30.random.sigs/sp.sp/2.run.SA.R data-raw/Alexandrov_2020/syn.many.types/sa.sa.96/1.run.SA.R data-raw/Alexandrov_2020/syn.many.types/sa.sa.COMPOSITE/3.run.SA.R data-raw/Alexandrov_2020/syn.many.types/sp.sa.COMPOSITE/4.run.SA.R data-raw/Alexandrov_2020/syn.many.types/sp.sp/2.run.SA.R data-raw/Alexandrov_2020/syn.pancreas/sa.sa.96/1.run.SA.R data-raw/Alexandrov_2020/syn.pancreas/sa.sa.COMPOSITE/3.run.SA.R data-raw/Alexandrov_2020/syn.pancreas/sp.sa.COMPOSITE/4.run.SA.R data-raw/Alexandrov_2020/syn.pancreas/sp.sp/2.run.SA.R data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.12.1990.3.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.12.1991.7.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.12.2004.2.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.12.2004.3.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.12.2004.5.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.12.2005.4.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.12.2005.8.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.12.2010.6.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.12.2024.4.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.12.2029.1.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.13.2197.10.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.13.2197.8.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.13.2199.7.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.13.2205.6.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.13.2213.10.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.13.2213.2.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.13.2213.5.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.13.2214.1.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.13.2214.9.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_DEMO/signature.L1W.L2H.LEGO96.Biliary.13.2215.9.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_SignatureAnalyzer/signature.DNP.primary.re_ordered.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_SignatureAnalyzer/signature.DNP.secondary.re_ordered.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_SignatureAnalyzer/signature.INDEL.primary.re_ordered.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_SignatureAnalyzer/signature.INDEL.secondary.re_ordered.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_SignatureAnalyzer/signature.SNV.primary.re_ordered.pdf data-raw/SignatureAnalyzer.052418/OUTPUT_SignatureAnalyzer/signature.SNV.secondary.re_ordered.pdf data-raw/SignatureAnalyzer.052418/SignatureAnalyzer.PCAWG.COMPOSITE-steve-questions.R data-raw/SignatureAnalyzer.052418/SignatureAnalyzer.PCAWG.COMPOSITE.R data-raw/SignatureAnalyzer.052418/SignatureAnalyzer.PCAWG.DNP.R data-raw/SignatureAnalyzer.052418/SignatureAnalyzer.PCAWG.INDEL.R data-raw/SignatureAnalyzer.052418/SignatureAnalyzer.PCAWG.function.R data-raw/SignatureAnalyzer.052418/SignatureAnalyzer.demo.R data-raw/SynSigRun_1.0.0.pdf data-raw/Wu_2022/1_scripts.for.SBS1SBS5/1_data_generation/SBS1SBS5.Gen.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/2_running_approaches_without_knowing_K/Prep.for.Running.EMu.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/2_running_approaches_without_knowing_K/Prep.for.Running.MultiModalMuSig.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/2_running_approaches_without_knowing_K/Prep.for.Running.helmsman.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/2_running_approaches_without_knowing_K/Run.MutationalPatterns.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/2_running_approaches_without_knowing_K/Run.SignatureAnalyzer.on.Linux.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/2_running_approaches_without_knowing_K/Run.SomaticSignatures.NMF.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/2_running_approaches_without_knowing_K/Run.hdp.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/2_running_approaches_without_knowing_K/Run.maftools.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/2_running_approaches_without_knowing_K/Run.mutSpec.NMF.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/2_running_approaches_without_knowing_K/Run.sigfit.EMu.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/2_running_approaches_without_knowing_K/Run.sigfit.NMF.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/2_running_approaches_without_knowing_K/Run.sigminer.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/2_running_approaches_without_knowing_K/Run.signeR.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/2_running_approaches_without_knowing_K/Run.tcsm.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/3_running_approaches_given_K/Prep.for.Running.EMu.exact.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/3_running_approaches_given_K/Prep.for.Running.MultiModalMuSig.exact.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/3_running_approaches_given_K/Prep.for.Running.helmsman.exact.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/3_running_approaches_given_K/Run.MutationalPatterns.exact.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/3_running_approaches_given_K/Run.SignatureAnalyzer.on.Linux.exact.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/3_running_approaches_given_K/Run.SomaticSignatures.NMF.exact.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/3_running_approaches_given_K/Run.hdp.exact.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/3_running_approaches_given_K/Run.maftools.exact.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/3_running_approaches_given_K/Run.mutSignatures.exact.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/3_running_approaches_given_K/Run.mutSpec.NMF.exact.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/3_running_approaches_given_K/Run.sigfit.EMu.exact.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/3_running_approaches_given_K/Run.sigfit.NMF.exact.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/3_running_approaches_given_K/Run.sigminer.exact.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/3_running_approaches_given_K/Run.signature.tools.lib.exact.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/3_running_approaches_given_K/Run.signeR.exact.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/3_running_approaches_given_K/Run.tcsm.exact.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/4_evaluation_without_knowing_K/Convert.EMu.Results.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/4_evaluation_without_knowing_K/Convert.MultiModalMuSig.Results.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/4_evaluation_without_knowing_K/Summarize.extr.attr.K.unknown.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/4_evaluation_without_knowing_K/mean.median.sd.mad.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/5_evaluation_given_K/Convert.EMu.Results.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/5_evaluation_given_K/Convert.MultiModalMuSig.Results.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/5_evaluation_given_K/Convert.signature.tools.lib.Results.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/5_evaluation_given_K/Summarize.extr.attr.K.given.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/5_evaluation_given_K/mean.median.sd.mad.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/6.join.combined.extraction.results.Wlicoxon.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/7_running_approaches_K_from_1_to_10/Prep.for.Running.EMu.fromOne.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/7_running_approaches_K_from_1_to_10/Prep.for.Running.MultiModalMuSig.fromOne.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/7_running_approaches_K_from_1_to_10/Prep.for.Running.helmsman.fromOne.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/7_running_approaches_K_from_1_to_10/Run.sigfit.EMu.fromOne.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/7_running_approaches_K_from_1_to_10/Run.sigfit.NMF.fromOne.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/7_running_approaches_K_from_1_to_10/Run.signeR.fromOne.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/8_evaluation_K_from_1_to_10/Convert.EMu.Results.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/8_evaluation_K_from_1_to_10/Convert.MultiModalMuSig.Results.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/8_evaluation_K_from_1_to_10/Linear.regression.cosine.similarity.combined.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/8_evaluation_K_from_1_to_10/Plot.Scaled.Manhattan.fixed.ylim.R data-raw/Wu_2022/1_scripts.for.SBS1SBS5/8_evaluation_K_from_1_to_10/Summarize.extr.attr.K.one.to.ten.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/2a1_running_approaches_K_from_1_to_10/Run.SparseSignatures.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/2a1_running_approaches_K_from_1_to_10/Run.mutSignatures.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/2a_running_approaches_without_knowing_K/Run.SparseSignatures.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/2a_running_approaches_without_knowing_K/Run.mutSignatures.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/2c_RunningApproachesForAttributionKnownSigs/Run.MutationalPatterns.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/2c_RunningApproachesForAttributionKnownSigs/Run.SignatureEstimation.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/2c_RunningApproachesForAttributionKnownSigs/Run.YAPSA.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/2c_RunningApproachesForAttributionKnownSigs/Run.decompTumor2Sig.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/2c_RunningApproachesForAttributionKnownSigs/Run.deconstructsigs.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/2c_RunningApproachesForAttributionKnownSigs/Run.mSigAct.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/2c_RunningApproachesForAttributionKnownSigs/Run.mutSignatures.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/2c_RunningApproachesForAttributionKnownSigs/Run.sigfit.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/2d_testing_MM_LDA_without_knowing_K/Prep.for.Running.MM.extra.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/2d_testing_MM_LDA_without_knowing_K/Prep.for.Running.MMLDA.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/2e_testing_MM_CTM_without_knowing_K/Prep.for.Running.MMCTM.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/2f_testing_MM_LDA_given_K/Prep.for.Running.MMLDA.Exact.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/2g_testing_MM_CTM_given_K/Prep.for.Running.MMCTM.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3a_evaluation_without_knowing_K/Linear.regression.CompositeMeasure.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3a_evaluation_without_knowing_K/Linear.regression.ExtractionMeasures.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3a_evaluation_without_knowing_K/Linear.regression.ExtractionMeasures.combined.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3a_evaluation_without_knowing_K/Linear.regression.ScaledManhattan.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3a_evaluation_without_knowing_K/Linear.regression.ScaledManhattan.combined.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3b_evaluation_given_K/Linear.regression.ExtractionMeasures.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3b_evaluation_given_K/Linear.regression.ExtractionMeasures.combined.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3b_evaluation_given_K/Linear.regression.ScaledManhattan.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3b_evaluation_given_K/Linear.regression.ScaledManhattan.combined.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3b_evaluation_given_K/Plot.Scaled.Manhattan.fixed.ylim.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3c_evaluation_attr_known_sigs/Summarize.attr.known.sigs.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3d_evaluation_MM_LDA_without_knowing_K/Convert.MultiModalMuSig.LDA.Results.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3d_evaluation_MM_LDA_without_knowing_K/Summarize.MM.LDA.K.unknown.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3e_evaluation_MM_CTM_without_knowing_K/Convert.MultiModalMuSig.CTM.Results.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3e_evaluation_MM_CTM_without_knowing_K/Summarize.MM.CTM.K.unknown.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3f_evaluation_MM_LDA_given_K/Convert.MultiModalMuSig.LDA.exact.Results.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3f_evaluation_MM_LDA_given_K/Summarize.MM.LDA.K.given.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3g_evaluation_MM_CTM_given_K/Convert.MultiModalMuSig.CTM.exact.Results.R data-raw/Wu_2022/2_additional.scripts.on.SBS1SBS5.datasets/3g_evaluation_MM_CTM_given_K/Summarize.MM.CTM.K.given.R data-raw/Wu_2022/Run.software.packages.for.SBS1SBS5.R man/BestSignatureAnalyzerResult.Rd man/CopyBestSignatureAnalyzerResult.Rd man/Diff4SynDataSets.Rd man/FixSASigNames.Rd man/InstallMutationalPatterns.Rd man/InstallSignatureEstimation.Rd man/InstallSomaticSignatures.Rd man/InstallSparseSignatures.Rd man/InstallYAPSA.Rd man/InstalldecompTumor2Sig.Rd man/InstalldeconstructSigs.Rd man/InstallmSigAct.Rd man/Installmaftools.Rd man/InstallmutSignatures.Rd man/Installsigfit.Rd man/Installsigminer.Rd man/InstallsigneR.Rd man/MapSPToSASignatureNamesInExposure.Rd man/MutationalSignatures.Rd man/RealExposures.Rd man/RunMutationalPatterns.Rd man/RunMutationalPatternsAttributeOnly.Rd man/RunSignatureAnalyzerAttribution.Rd man/RunSignatureAnalyzerOnFile.Rd man/RunSignatureEstimationQPAttributeOnly.Rd man/RunSignatureEstimationSAAttributeOnly.Rd man/RunSomaticSignatures.Rd man/RunSparseSignatures.Rd man/RunYAPSAAttributeOnly.Rd man/RundecompTumor2SigAttributeOnly.Rd man/RundeconstructSigsAttributeOnly.Rd man/RunhdpLessHier.Rd man/RunmSigActAttributeOnly.Rd man/Runmaftools.Rd man/RunmutSignatures.Rd man/RunmutSignaturesAttributeOnly.Rd man/RunmutSpec.Rd man/Runsigfit.Rd man/RunsigfitAttributeOnly.Rd man/Runsigminer.Rd man/RunsigneR.Rd man/Runtcsm.Rd man/SAMultiRunOneCatalog.Rd man/SignatureAnalyzer4MatchedCatalogs.Rd man/SignatureAnalyzerOneRun.Rd man/SignatureAnalyzerPrepHyper1Secondary.Rd man/SignatureAnalyzerPrepHyper4.Rd man/SourceSignatureAnalyzerCode.Rd man/SynSigRun.Rd man/make.heldout.obj.Rd tests/SA.code/SignatureAnalyzer.PCAWG.function.R tests/SBS96/SBS96_selection_plot.pdf tests/testthat.R tests/testthat/sa.COMP.exome.test.input/Create.SECONDARY.input.R tests/testthat/sa.COMP.exome.test.ref.output/Create.SECONDARY.input.R tests/testthat/sa.COMP.exome.test.ref.output/Split.hyper.vs.non.hyper.R tests/testthat/test.mutational_signature_similarity.R tests/testthat/test.run.signatureanalyzer.R tests/testthat/test.sa.getbest.R tests/testthat/test.summarize.one.dir.R