Files in MesKit

A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations

MesKit.docker.md README.md

NAMESPACE

DESCRIPTION

LICENSE

R/compareTree.R R/readMaf.R R/drawVafCluster.R R/calJSI.R R/compareCCF.R R/calNeiDist.R R/plotMutProfile.R R/methods.R R/plotCNA.R R/plotPowerLaw.R R/readCCF.R R/defineMutType.R R/phyloTreeAnno.R R/ccfAUC.R R/subTriMatrix.R R/mutHeatmap.R R/getPhyloTree.R R/cna2gene.R R/Meskit.R R/testNeutral.R R/readGistic.R R/fitSignatures.R R/classifyMut.R R/readSegment.R R/phyloTreeObject.R R/subPhyloTree.R R/calFst.R R/mutTrunkBranch.R R/mathScore.R R/plotCorr.R R/triMatrix.R R/mutCluster.R R/copyNumberFilter.R R/plotMutSigProfile.R R/plotPhyloTree.R R/classS4.R R/getMutMatrix.R R/readPhyloTree.R R/subMaf.R R/validation.R

inst/NEWS

inst/doc/MesKit.R inst/doc/MesKit.Rmd

inst/doc/MesKit.html

inst/shiny/ui.R inst/shiny/server.R

inst/shiny/www/main.css

inst/shiny/www/image/logo.jpg

inst/shiny/www/image/MesKit_workflow.png

inst/shiny/www/image/button.png

inst/shiny/www/css/main.css

inst/shiny/dom/maf.csv

inst/shiny/dom/ccf.CSV

inst/extdata/signatures.nature2013.rds

inst/extdata/CRC_HZ.seg.txt

inst/extdata/COREAD_del_genes.conf_99.txt

inst/extdata/CRC_HZ.maf

inst/extdata/IntOGen-DriverGenes_COREAD.tsv

inst/extdata/CRC_HZ.ccf.tsv

inst/extdata/CRC_HZ.clin.txt

inst/extdata/signatures.cosmic.rds

inst/extdata/signatures.etiology.rds

inst/extdata/signatures.exome.cosmic.v3.may2019.rds

inst/extdata/COREAD_all_lesions.conf_99.txt

inst/extdata/COREAD_amp_genes.conf_99.txt

inst/script/DATASETS

build/vignette.rds

vignettes/logo.png

vignettes/MesKit.Rmd

vignettes/MesKit_workflow.png

man/getMafRef.Rd man/getPhyloTreeTsbLabel.Rd man/MafList-class.Rd man/ccfAUC.Rd man/getMutBranches.Rd man/compareTree.Rd man/getBinaryMatrix.Rd man/testNeutral.Rd man/mutHeatmap.Rd man/triMatrix.Rd man/readMaf.Rd man/getMafData.Rd man/plotPhyloTree.Rd man/plotMutProfile.Rd man/Maf-class.Rd man/getBootstrapValue.Rd man/getPhyloTreePatient.Rd man/getMafPatient.Rd man/mutTrunkBranch.Rd man/getBranchType.Rd man/calJSI.Rd man/getPhyloTreeRef.Rd man/mathScore.Rd man/compareCCF.Rd man/mutCluster.Rd man/getNonSyn_vc.Rd man/readSegment.Rd man/getCCFMatrix.Rd man/subMaf.Rd man/plotCNA.Rd man/phyloTreeList-class.Rd man/getSampleInfo.Rd man/plotMutSigProfile.Rd man/calNeiDist.Rd man/classifyMut.Rd man/runMesKit.Rd man/calFst.Rd man/phyloTree-class.Rd man/cna2gene.Rd man/getPhyloTree.Rd man/getTree.Rd man/fitSignatures.Rd man/getTreeMethod.Rd

MesKit documentation built on March 28, 2021, 6 p.m.