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