NAMESPACE

# Generated by roxygen2: do not edit by hand

export("%!in%")
export("%>%")
export("consensus<-")
export("consensusPhylo<-")
export("distMat<-")
export("graph<-")
export("phylo<-")
export(.countBreakpoints)
export(.invft)
export(.multipcf)
export(.quiet)
export(CopyKit)
export(bincounts)
export(calcConsensus)
export(calcInteger)
export(calcRatios)
export(combine.func)
export(compactMulti)
export(consensus)
export(consensusPhylo)
export(copykit_example)
export(copykit_example_filtered)
export(distMat)
export(doMultiPCF)
export(expandMulti)
export(findAneuploidCells)
export(findClusters)
export(findMarksMulti)
export(findOutliers)
export(findSuggestedK)
export(findVariableGenes)
export(find_scaffold_genes)
export(getArmandChromStop)
export(getArms)
export(getMad)
export(graph)
export(hdbscanCBI)
export(inferMrca)
export(knnSmooth)
export(l2e.normal.sd)
export(leidenCBI)
export(logNorm)
export(louvainCBI)
export(markMultiPotts)
export(medianFilter)
export(mergeLevels)
export(mock_bincounts)
export(multiPCFcompact)
export(numericArms)
export(numericChrom)
export(ocean.balance)
export(ocean_balance_hex)
export(overdispersion)
export(parCor)
export(phylo)
export(plotAlluvial)
export(plotConsensusLine)
export(plotFreq)
export(plotGeneCopy)
export(plotHeatmap)
export(plotMetrics)
export(plotPca)
export(plotPhylo)
export(plotRatio)
export(plotScree)
export(plotSuggestedK)
export(plotUmap)
export(plotVariableGenes)
export(pullOutContent)
export(ratios)
export(runConsensusPhylo)
export(runCountReads)
export(runDistMat)
export(runFastMultiPCF)
export(runMetrics)
export(runMultiPcfSubset)
export(runPca)
export(runPhylo)
export(runSegmentation)
export(runUmap)
export(runVarbin)
export(runVst)
export(sawMarkM)
export(segment_ratios)
export(selectFastMultiPcf)
export(subclones_pal)
export(superclones_pal)
exportClasses(CopyKit)
exportClasses(igraph)
exportMethods("consensus<-")
exportMethods("consensusPhylo<-")
exportMethods("distMat<-")
exportMethods("graph<-")
exportMethods("phylo<-")
exportMethods(bincounts)
exportMethods(consensus)
exportMethods(consensusPhylo)
exportMethods(distMat)
exportMethods(graph)
exportMethods(phylo)
exportMethods(ratios)
exportMethods(segment_ratios)
exportMethods(show)
import(ComplexHeatmap)
import(ggalluvial)
import(ggplot2)
import(ggtree)
import(methods)
import(shiny)
importClassesFrom(S4Vectors,DataFrame)
importClassesFrom(S4Vectors,SimpleList)
importClassesFrom(SingleCellExperiment,SingleCellExperiment)
importClassesFrom(SummarizedExperiment,RangedSummarizedExperiment)
importFrom(BiocGenerics,`%in%`)
importFrom(BiocGenerics,subset)
importFrom(BiocNeighbors,findKNN)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpparam)
importFrom(DNAcopy,CNA)
importFrom(DNAcopy,segment)
importFrom(DNAcopy,smooth.CNA)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(Rsubread,featureCounts)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(SingleCellExperiment,"reducedDim<-")
importFrom(SingleCellExperiment,reducedDim)
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(SummarizedExperiment,seqnames)
importFrom(ape,Nnode)
importFrom(ape,Ntip)
importFrom(ape,drop.tip)
importFrom(ape,fastme.bal)
importFrom(ape,ladderize)
importFrom(ape,nj)
importFrom(ape,root.phylo)
importFrom(bluster,makeSNNGraph)
importFrom(circlize,colorRamp2)
importFrom(dbscan,hdbscan)
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,count)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,pull)
importFrom(dplyr,relocate)
importFrom(dplyr,rename)
importFrom(dplyr,right_join)
importFrom(dplyr,row_number)
importFrom(dplyr,select)
importFrom(dplyr,slice_min)
importFrom(dplyr,summarise)
importFrom(dplyr,ungroup)
importFrom(forcats,fct_reorder)
importFrom(fpc,clusterboot)
importFrom(ggalluvial,geom_stratum)
importFrom(ggalluvial,stat_stratum)
importFrom(ggnewscale,new_scale_color)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,colors)
importFrom(gtools,mixedsort)
importFrom(igraph,cluster_leiden)
importFrom(igraph,cluster_louvain)
importFrom(igraph,membership)
importFrom(magrittr,"%>%")
importFrom(miniUI,gadgetTitleBar)
importFrom(miniUI,miniContentPanel)
importFrom(miniUI,miniPage)
importFrom(mixtools,normalmixEM)
importFrom(scales,hue_pal)
importFrom(scales,percent_format)
importFrom(scquantum,ploidy.inference)
importFrom(scquantum,timeseries.iod)
importFrom(shiny,checkboxGroupInput)
importFrom(shiny,fillCol)
importFrom(shiny,plotOutput)
importFrom(shiny,stopApp)
importFrom(stats,ansari.test)
importFrom(stats,approx)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,lowess)
importFrom(stats,median)
importFrom(stats,prcomp)
importFrom(stats,rnorm)
importFrom(stats,rpois)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,wilcox.test)
importFrom(tidyr,complete)
importFrom(tidyr,gather)
importFrom(tidyr,pivot_wider)
importFrom(uwot,umap)
importFrom(viridis,viridis)
importFrom(withr,with_seed)
importMethodsFrom(SingleCellExperiment,show)
importMethodsFrom(SummarizedExperiment,assay)
importMethodsFrom(SummarizedExperiment,colData)
importMethodsFrom(SummarizedExperiment,rowRanges)