Files in PoisonAlien/maftools
Summarize, Analyze and Visualize MAF Files

.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/ClinicalEnrichment.R R/TrinucleotideMatrix.R R/addOncoprint.R R/annovarToMaf.R R/clusterScore.R R/coOncoplot.R R/countMatrix.R R/dashboard.R R/detectCP.R R/domainSummary.R R/extractSignatures.R R/filterCopyNumber.R R/fisherCorrect.R R/forestPlot.R R/geneCloud.R R/genesToBarcodes.R R/getOncoPlot.R R/get_lp_data.R R/gisticBubblePlot.R R/gisticChromPlot.R R/gisticObject.R R/gisticOncoPlot.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/mafSuvival.R R/maf_methods.R R/mathScore.R R/oncodrive.R R/oncomatrix.R R/oncoplot.R R/oncostrip.R R/oncotate.R R/pancanAnalysis.R R/plotApobecDiff.R R/plotClinicalEnrichment.R R/plotClusters.R R/plotMafSummary.R R/plotOncodriveClust.R R/plotSignatures.R R/plotTiTv.R R/plot_cbs_segs.R R/plot_vaf.R R/prepareMutSig.R R/rainfallPlot.R R/readGistic.R R/readSegs.R R/read_maf_dt.R R/refineClusters.R R/repelPoints.R R/signatureCorrelation.R R/snpMatrix.R R/somaticInteractions.R R/subsetMaf.R R/summarizeGistic.R R/summarizeMaf.R R/tcgacompare.R R/titv.R R/validateMaf.R R/writeGisticSummary.R R/wrteMafSummary.R README.md
inst/CITATION
inst/NEWS
inst/extdata/APL_primary.maf.gz
inst/extdata/APL_relapse.maf.gz
inst/extdata/LAML_sig_genes.txt.gz
inst/extdata/TCGA.AB.3009.hg19.seg.txt
inst/extdata/all_lesions.conf_99.txt
inst/extdata/amp_genes.conf_99.txt
inst/extdata/coad.maf.gz
inst/extdata/del_genes.conf_99.txt
inst/extdata/ensGenes.txt.gz
inst/extdata/hugo_to_mutSigSymbol.txt.gz
inst/extdata/pancan.txt.gz
inst/extdata/prot_len.txt.gz
inst/extdata/protein_domains.RDs
inst/extdata/scores.gistic
inst/extdata/signatures.txt
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
maftools.Rproj
man/GISTIC-class.Rd man/MAF-class.Rd man/annovarToMaf.Rd man/clinicalEnrichment.Rd man/coOncoplot.Rd man/extractSignatures.Rd man/forestPlot.Rd man/geneCloud.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/gisticOncoPlot.Rd man/icgcSimpleMutationToMAF.Rd man/inferHeterogeneity.Rd man/lollipopPlot.Rd man/lollipopPlot2.Rd man/mafCompare.Rd man/mafSummary.Rd man/mafSurvival.Rd man/math.score.Rd man/mutCountMatrix.Rd man/oncodrive.Rd man/oncoplot.Rd man/oncostrip.Rd man/oncotate.Rd man/pancanComparison.Rd man/pfamDomains.Rd man/plotApobecDiff.Rd man/plotCBSsegments.Rd man/plotClusters.Rd man/plotEnrichmentResults.Rd man/plotOncodrive.Rd man/plotSignatures.Rd man/plotTiTv.Rd man/plotVaf.Rd man/plotmafSummary.Rd man/prepareMutSig.Rd man/rainfallPlot.Rd man/read.maf.Rd man/readGistic.Rd man/signatureEnrichment.Rd man/somaticInteractions.Rd man/subsetMaf.Rd man/tcgaCompare.Rd man/titv.Rd man/trinucleotideMatrix.Rd man/write.GisticSummary.Rd man/write.mafSummary.Rd
vignettes/corp-styles.css
vignettes/maftools.Rmd
vignettes/maftools.png
vignettes/overview.png
PoisonAlien/maftools documentation built on April 21, 2018, 5:19 p.m.