NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(mutate,admat)
S3method(mutate,admat.2)
S3method(mutate,admat.3)
S3method(mutate,column)
S3method(mutate,n.columns)
S3method(mutate,n.columns.clusterprob)
export(calcSubcloneProportions)
export(calcTreeScores)
export(calculateTreeScoreMutations)
export(collectBestKChains)
export(colorScheme)
export(enumerateSpanningTreesModified)
export(estimateClusterAssignments)
export(estimateICN)
export(estimateMCFs)
export(estimateMultiplicity)
export(estimateMultiplicityMatrix)
export(filterEdgesBasedOnCCFs)
export(generateAllTrees)
export(importFiles)
export(mcmcMain)
export(mergeSetChains)
export(plotChainsMCF)
export(plotClusterAssignmentProbVertical)
export(plotEnsembleTree)
export(plotMCFViolin)
export(plotSubcloneBar)
export(plotSubclonePie)
export(plotTree)
export(prepareGraph)
export(runMCMCForAllBoxes)
export(separateMutationsBySamplePresence)
export(writeClusterAssignmentsTable)
export(writeClusterMCFsTable)
export(writeIcnTable)
export(writeMultiplicityTable)
export(writeSetKTable)
import(UpSetR)
import(cluster)
import(dplyr)
import(ggmcmc)
import(ggplot2)
import(igraph)
import(magrittr)
import(methods)
import(readr)
import(rjags)
import(stringr)
import(tibble)
import(tidyr)
import(tidyverse)
import(viridis)
importFrom(epiR,epi.betabuster)
importFrom(stringr,str_replace)