Man pages for WuyangFF95/SynSigRun
Run Mutational Signature Analysis Software Packages Using Mutational Spectra generated by SynSigGen
| BestSignatureAnalyzerResult | Find the best SignatureAnalyzer result over a set of output... |
| CopyBestSignatureAnalyzerResult | Find the SignatureAnalyzer results directory with the best... |
| Diff4SynDataSets | diff new directory / files against regression data for... |
| FixSASigNames | Standardize SignatureAnalyzer signature names |
| InstalldecompTumor2Sig | Install decompTumor2Sig from Bioconductor |
| InstalldeconstructSigs | Install deconstructSigs from CRAN |
| Installmaftools | Install maftools from Bioconductor, and its dependent... |
| InstallmSigAct | Install mSigAct from GitHub |
| InstallMutationalPatterns | Install MutationalPatterns from Bioconductor, and its... |
| InstallmutSignatures | Install mutSignatures from github |
| Installsigfit | Install sigfit from GitHub, and its dependent package, rstan. |
| Installsigminer | Install sigminer from Bioconductor, also installing its... |
| InstallSignatureEstimation | Install SignatureEstimation package from URL source. |
| InstallsigneR | Install signeR from Bioconductor |
| InstallSomaticSignatures | Install SomaticSignatures from Bioconductor, also installing... |
| InstallSparseSignatures | Install SparseSignatures from Bioconductor |
| InstallYAPSA | Install YAPSA package from Bioconductor. |
| make.heldout.obj | tcsm's internal function to calculate likelihood for each 'K'... |
| MapSPToSASignatureNamesInExposure | With the signatures represented in a matrix of exposures,... |
| MutationalSignatures | Reference mutational signature profiles from PCAWG7. |
| RealExposures | Real exposure (signature attributions) from SignatureAnalyzer... |
| RundecompTumor2SigAttributeOnly | Run decompTumor2Sig attribution on a spectra catalog file and... |
| RundeconstructSigsAttributeOnly | Run deconstructSigs attribution on a spectra catalog file and... |
| RunhdpLessHier | Run hdp extraction and attribution on a spectra catalog file |
| Runmaftools | Run maftools extraction ONLY on a spectra catalog file |
| RunmSigActAttributeOnly | Run mSigAct attribution on a spectra catalog file and known... |
| RunMutationalPatterns | Run MutationalPatterns extraction and attribution on a... |
| RunMutationalPatternsAttributeOnly | Run MutationalPatterns attribution on a spectra catalog file... |
| RunmutSignatures | Run mutSignatures extraction and attribution on a spectra... |
| RunmutSignaturesAttributeOnly | Run mutSignatures attribution on a spectra catalog file and... |
| RunmutSpec | Run mutSpec extraction and attribution on a spectra catalog... |
| Runsigfit | Run sigfit extraction and attribution on a spectra catalog... |
| RunsigfitAttributeOnly | Run sigfit attribution on a spectra catalog file and known... |
| Runsigminer | Run sigminer extraction and attribution on a spectra catalog... |
| RunSignatureAnalyzerAttribution | Run SignatureAnalyzer attribution on a catalog file and... |
| RunSignatureAnalyzerOnFile | Run SignatureAnalyzer on a file containing a catalog AFTER... |
| RunSignatureEstimationQPAttributeOnly | Run SignatureEstimation Quadratic Programming (QP)... |
| RunSignatureEstimationSAAttributeOnly | Run SignatureEstimation Simulated Annealing (SA) attribution... |
| RunsigneR | Run signeR extraction and attribution on a spectra catalog... |
| RunSomaticSignatures | Run SomaticSignatures.NMF extraction and attribution on a... |
| RunSparseSignatures | Run SparseSignatures extraction and attribution on a spectra... |
| Runtcsm | Run tcsm extraction and attribution on a spectra catalog file |
| RunYAPSAAttributeOnly | Run YAPSA attribution on a spectra catalog file and known... |
| SAMultiRunOneCatalog | Run SignatureAnalyzer many times on one catalog and put... |
| SignatureAnalyzer4MatchedCatalogs | Run SignatureAnalyzer on 4 coordinated data sets and put... |
| SignatureAnalyzerOneRun | Source SignatureAnalyzer and run it once on a single data set... |
| SignatureAnalyzerPrepHyper1Secondary | Prepare the "hypermutated" segment (a.k.a "Secondary" segment... |
| SignatureAnalyzerPrepHyper4 | Prepare the "hypermutated" segment (a.k.a "Secondary" segment... |
| SourceSignatureAnalyzerCode | Source SignatureAnalyzer Codes. |
| SynSigRun | 'SynSigRun': An easy-to-use package for non-experts which... |
