NAMESPACE

# Generated by roxygen2: do not edit by hand

export(calFst)
export(calJSI)
export(calNeiDist)
export(ccfAUC)
export(classifyMut)
export(cna2gene)
export(compareCCF)
export(compareTree)
export(fitSignatures)
export(getPhyloTree)
export(mathScore)
export(mutCluster)
export(mutHeatmap)
export(mutTrunkBranch)
export(plotCNA)
export(plotMutProfile)
export(plotMutSigProfile)
export(plotPhyloTree)
export(readMaf)
export(readSegment)
export(runMesKit)
export(subMaf)
export(testNeutral)
export(triMatrix)
exportClasses(Maf)
exportClasses(MafList)
exportClasses(phyloTree)
exportClasses(phyloTreeList)
exportMethods(getBinaryMatrix)
exportMethods(getBootstrapValue)
exportMethods(getBranchType)
exportMethods(getCCFMatrix)
exportMethods(getMafData)
exportMethods(getMafPatient)
exportMethods(getMafRef)
exportMethods(getMutBranches)
exportMethods(getNonSyn_vc)
exportMethods(getPhyloTreePatient)
exportMethods(getPhyloTreeRef)
exportMethods(getPhyloTreeTsbLabel)
exportMethods(getSampleInfo)
exportMethods(getTree)
exportMethods(getTreeMethod)
import(ComplexHeatmap)
import(RColorBrewer)
import(ape)
import(circlize)
import(cowplot)
import(dplyr)
import(ggplot2)
import(ggrepel)
import(ggridges)
import(mclust)
import(methods)
import(phangorn)
import(tidyr)
importFrom(Biostrings,end)
importFrom(Biostrings,getSeq)
importFrom(Biostrings,start)
importFrom(S4Vectors,Rle)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,foverlaps)
importFrom(data.table,fread)
importFrom(data.table,rbindlist)
importFrom(data.table,setkey)
importFrom(grDevices,boxplot.stats)
importFrom(grDevices,colors)
importFrom(pracma,lsqnonneg)
importFrom(stats,approxfun)
importFrom(stats,fisher.test)
importFrom(stats,integrate)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,qnorm)
importFrom(utils,combn)