├── .Rbuildignore ├── .github ├── ISSUE_TEMPLATE │ └── report-an-issue.md └── workflows │ ├── R-CMD-check.yaml │ └── stale_bot.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── ClinicalEnrichment.R ├── TrinucleotideMatrix.R ├── addOncoprint.R ├── annovarToMaf.R ├── bamrcBAM.R ├── bamrcCounting.R ├── bamreadcounts.R ├── bamreadcountsValidation.R ├── cancerhotspots.R ├── cancerhsAggr.R ├── clusterScore.R ├── coBarplot.R ├── coGisticChromPlotV.R ├── coOncoplot.R ├── compareSignatures.R ├── countMatrix.R ├── dashboard.R ├── detect_kataegis.R ├── domainSummary.R ├── driverBP.R ├── drugInteractions.R ├── estimateSignatures.R ├── estimate_binconf.R ├── extractSignatures.R ├── filterCopyNumber.R ├── filterMaf.R ├── fisherCorrect.R ├── forestPlot.R ├── genesToBarcodes.R ├── get_lp_data.R ├── gisticBubblePlot.R ├── gisticChromPlot.R ├── gisticComapre.R ├── gisticObject.R ├── gisticOncoPlot.R ├── gtSNPs.R ├── icgc_to_maf.R ├── inferTumHetero.R ├── lollipopPlot.R ├── lollipopPlot2.R ├── mafCompare.R ├── mafGeneSummary.R ├── mafObjects.R ├── mafSurvGroup.R ├── mafSuvival.R ├── maf_methods.R ├── mafbarplot.R ├── mathScore.R ├── mergeMafs.R ├── oncoPathway.R ├── oncodrive.R ├── oncomatrix.R ├── oncoplot.R ├── oncostrip.R ├── plotApobecDiff.R ├── plotClinicalEnrichment.R ├── plotClusters.R ├── plotCophenetic.R ├── plotMafSummary.R ├── plotOncodriveClust.R ├── plotPathways.R ├── plotPathways2.R ├── plotProtein.R ├── plotSignatures.R ├── plotTiTv.R ├── plot_cbs_segs.R ├── plot_mostdepth.R ├── plot_mostdepth_tn.R ├── plot_vaf.R ├── prepAscat.R ├── prepAscat_t.R ├── prepareMutSig.R ├── print_mat.R ├── rainfallPlot.R ├── readGistic.R ├── readSegs.R ├── read_maf_dt.R ├── refineClusters.R ├── repelPoints.R ├── sample_swap.R ├── segSummarize.R ├── segment_logR.R ├── setMaf.R ├── signatureCorrelation.R ├── snpMatrix.R ├── somaticInteractions.R ├── subsetMaf.R ├── summarizeGistic.R ├── summarizeMaf.R ├── survGroup.R ├── tcga.R ├── tcgaLoad.R ├── tcgacompare.R ├── titv.R ├── tmb.R ├── treeplot.R ├── vafComapre.R ├── validateMaf.R ├── writeGisticSummary.R └── wrteMafSummary.R ├── README.md ├── inst ├── CITATION ├── NEWS.md ├── extdata │ ├── APL_primary.maf.gz │ ├── APL_relapse.maf.gz │ ├── BP_SMGs.txt.gz │ ├── LAML_CBS_segments.tsv.gz │ ├── LAML_sig_genes.txt.gz │ ├── SBS_signatures.RDs │ ├── SBS_v34_signatures.RDs │ ├── TCGA.AB.3009.hg19.seg.txt │ ├── all_lesions.conf_99.txt │ ├── amp_genes.conf_99.txt │ ├── brca.maf.gz │ ├── cancerhotspots_v2_GRCh37.tsv │ ├── cancerhotspots_v2_GRCh38.tsv │ ├── cancerhotspots_v2_hg19.tsv │ ├── cancerhotspots_v2_hg38.tsv │ ├── categories.tsv.gz │ ├── del_genes.conf_99.txt │ ├── drugs.tsv.gz │ ├── ensGenes.txt.gz │ ├── hg19_cytobands.tsv.gz │ ├── hg19_smash_snps.tsv.gz │ ├── hg38_cytobands.tsv.gz │ ├── hg38_smash_snps.tsv.gz │ ├── hugo_to_mutSigSymbol.txt.gz │ ├── legacy_signatures.RDs │ ├── oncogenic_sig_patwhays.tsv │ ├── pancan.txt.gz │ ├── prot_len.txt.gz │ ├── protein_domains.RDs │ ├── scores.gistic │ ├── simple_somatic_mutation.open.ESCA-CN.sample.tsv.gz │ ├── tcga_cohort.txt.gz │ ├── tcga_laml.maf.gz │ ├── tcga_laml_annot.tsv │ ├── variants.hg19_multianno.txt │ └── variants.tsv └── old_news ├── maftools.Rproj ├── man ├── GISTIC-class.Rd ├── MAF-class.Rd ├── MAF.Rd ├── annovarToMaf.Rd ├── bamreadcounts.Rd ├── cancerhotspots.Rd ├── cancerhotspotsAggr.Rd ├── clinicalEnrichment.Rd ├── coBarplot.Rd ├── coGisticChromPlot.Rd ├── coOncoplot.Rd ├── compareSignatures.Rd ├── drugInteractions.Rd ├── estimateSignatures.Rd ├── extractSignatures.Rd ├── filterMaf.Rd ├── forestPlot.Rd ├── genesToBarcodes.Rd ├── genotypeMatrix.Rd ├── getClinicalData.Rd ├── getCytobandSummary.Rd ├── getFields.Rd ├── getGeneSummary.Rd ├── getSampleSummary.Rd ├── gisticBubblePlot.Rd ├── gisticChromPlot.Rd ├── gisticCompare.Rd ├── gisticOncoPlot.Rd ├── gtMarkers.Rd ├── icgcSimpleMutationToMAF.Rd ├── inferHeterogeneity.Rd ├── lollipopPlot.Rd ├── lollipopPlot2.Rd ├── maf2mae.Rd ├── mafCompare.Rd ├── mafSummary.Rd ├── mafSurvGroup.Rd ├── mafSurvival.Rd ├── mafbarplot.Rd ├── math.score.Rd ├── merge_mafs.Rd ├── mutCountMatrix.Rd ├── oncodrive.Rd ├── oncoplot.Rd ├── oncostrip.Rd ├── pathways.Rd ├── pfamDomains.Rd ├── plotApobecDiff.Rd ├── plotCBSsegments.Rd ├── plotClusters.Rd ├── plotCophenetic.Rd ├── plotEnrichmentResults.Rd ├── plotMosdepth.Rd ├── plotMosdepth_t.Rd ├── plotOncodrive.Rd ├── plotPathways.Rd ├── plotProtein.Rd ├── plotSignatures.Rd ├── plotTiTv.Rd ├── plotVaf.Rd ├── plotmafSummary.Rd ├── prepAscat.Rd ├── prepAscat_t.Rd ├── prepareMutSig.Rd ├── rainfallPlot.Rd ├── read.maf.Rd ├── readGistic.Rd ├── sampleSwaps.Rd ├── segSummarize.Rd ├── segmentLogR.Rd ├── setMaf.Rd ├── signatureEnrichment.Rd ├── somaticInteractions.Rd ├── subsetMaf.Rd ├── survGroup.Rd ├── tcgaAvailable.Rd ├── tcgaCompare.Rd ├── tcgaDriverBP.Rd ├── tcgaLoad.Rd ├── titv.Rd ├── tmb.Rd ├── trinucleotideMatrix.Rd ├── vafCompare.Rd ├── write.GisticSummary.Rd └── write.mafSummary.Rd ├── scripts ├── compile_snp6.R ├── 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