# Generated by roxygen2: do not edit by hand

export("colTree<-")
export("colTreeNames<-")
export("referenceSeq<-")
export("rowTree<-")
export("rowTreeNames<-")
export(LinkDataFrame)
export(TreeSummarizedExperiment)
export(addLabel)
export(aggTSE)
export(aggValue)
export(asLeaf)
export(asPhylo)
export(changeTree)
export(colLinks)
export(colTree)
export(colTreeNames)
export(convertNode)
export(countLeaf)
export(countNode)
export(detectLoop)
export(distNode)
export(findAncestor)
export(findChild)
export(findDescendant)
export(findOS)
export(findSibling)
export(isLeaf)
export(joinNode)
export(makeTSE)
export(matTree)
export(printNode)
export(referenceSeq)
export(resolveLoop)
export(rowLinks)
export(rowTree)
export(rowTreeNames)
export(shareNode)
export(showNode)
export(signalNode)
export(subsetByLeaf)
export(subsetByNode)
export(toTree)
export(trackNode)
export(transNode)
export(unionLeaf)
exportClasses(LinkDataFrame)
exportClasses(TreeSummarizedExperiment)
exportMethods("[")
exportMethods("[<-")
exportMethods("colTree<-")
exportMethods("colTreeNames<-")
exportMethods("colnames<-")
exportMethods("referenceSeq<-")
exportMethods("rowTree<-")
exportMethods("rowTreeNames<-")
exportMethods("rownames<-")
exportMethods(cbind)
exportMethods(colLinks)
exportMethods(colTree)
exportMethods(colTreeNames)
exportMethods(rbind)
exportMethods(referenceSeq)
exportMethods(rowLinks)
exportMethods(rowTree)
exportMethods(rowTreeNames)
exportMethods(subsetByLeaf)
exportMethods(subsetByNode)
exportMethods(updateObject)
exportMethods(vertical_slot_names)
import(S4Vectors)
import(SingleCellExperiment)
import(methods)
importClassesFrom(S4Vectors,DataFrame)
importClassesFrom(SingleCellExperiment,SingleCellExperiment)
importClassesFrom(SummarizedExperiment,RangedSummarizedExperiment)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(BiocParallel,bplapply)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,DNAStringSetList)
importFrom(IRanges,relist)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,head)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,tail)
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,assays)
importFrom(ape,keep.tip)
importFrom(ape,reorder.phylo)
importFrom(ape,rtree)
importFrom(dplyr,'%>%')
importFrom(dplyr,arrange_all)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_if)
importFrom(dplyr,row_number)
importFrom(methods,as)
importFrom(methods,callNextMethod)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,setOldClass)
importFrom(rlang,.data)
importFrom(stats,reorder)
importFrom(stats,setNames)
importFrom(treeio,as.phylo)
importFrom(utils,flush.console)
importMethodsFrom(SingleCellExperiment,show)
importMethodsFrom(SummarizedExperiment,rbind)
