TreeeSummarizedExperiment-package	TreeeSummarizedExperiment-package
.all_equal_in_list	dot-all_equal_in_list
.all_have_DNAStringSet	dot-all_have_DNAStringSet
.all_have_DNAStringSetList	dot-all_have_DNAStringSetList
.all_nonnull_in_list	dot-all_nonnull_in_list
.all_null_in_list	dot-all_null_in_list
.any_null_in_list	dot-any_null_in_list
.auto_rename_list	dot-auto_rename_list
.bind_link_tree	dot-bind_link_tree
.is_equal_link	dot-is_equal_link
.match_phylo	dot-match_phylo
.match_phylo_list	dot-match_phylo_list
.match_x_dupY	dot-match_x_dupY
.name_y_with_x	dot-name_y_with_x
.numeric_ij	dot-numeric_ij
.rbind_refSeq	dot-rbind_refSeq
.replace_link_tree_1d	dot-replace_link_tree_1d
.update_whichTree	dot-update_whichTree
addLabel	addLabel
aggTSE	aggTSE
aggValue	aggValue
asLeaf	asLeaf
cbind,TreeSummarizedExperiment-method	TreeSummarizedExperiment-combine
changeTree	changeTree
colLinks	TreeSummarizedExperiment-accessor
colLinks,TreeSummarizedExperiment-method	TreeSummarizedExperiment-accessor
colnames<-,TreeSummarizedExperiment-method	TreeSummarizedExperiment-accessor
colTree	TreeSummarizedExperiment-accessor
colTree,TreeSummarizedExperiment-method	TreeSummarizedExperiment-accessor
colTree<-	TreeSummarizedExperiment-accessor
colTree<-,TreeSummarizedExperiment-method	TreeSummarizedExperiment-accessor
colTreeNames	TreeSummarizedExperiment-accessor
colTreeNames,TreeSummarizedExperiment-method	TreeSummarizedExperiment-accessor
colTreeNames<-	TreeSummarizedExperiment-accessor
colTreeNames<-,TreeSummarizedExperiment-method	TreeSummarizedExperiment-accessor
convertNode	convertNode
countLeaf	countLeaf
countNode	countNode
detectLoop	detectLoop
distNode	distNode
findAncestor	findAncestor
findChild	findChild
findDescendant	findDescendant
findOS	findDescendant
findSibling	findSibling
isLeaf	isLeaf
joinNode	joinNode
LinkDataFrame	LinkDataFrame-constructor
LinkDataFrame-class	LinkDataFrame-class
LinkDataFrame-constructor	LinkDataFrame-constructor
makeTSE	makeTSE
matTree	matTree
phylo	phylo
printNode	printNode
rbind,TreeSummarizedExperiment-method	TreeSummarizedExperiment-combine
referenceSeq	TreeSummarizedExperiment-accessor
referenceSeq,TreeSummarizedExperiment-method	TreeSummarizedExperiment-accessor
referenceSeq<-	TreeSummarizedExperiment-accessor
referenceSeq<-,TreeSummarizedExperiment-method	TreeSummarizedExperiment-accessor
resolveLoop	resolveLoop
rowLinks	TreeSummarizedExperiment-accessor
rowLinks,TreeSummarizedExperiment-method	TreeSummarizedExperiment-accessor
rownames<-,TreeSummarizedExperiment-method	TreeSummarizedExperiment-accessor
rowTree	TreeSummarizedExperiment-accessor
rowTree,TreeSummarizedExperiment-method	TreeSummarizedExperiment-accessor
rowTree<-	TreeSummarizedExperiment-accessor
rowTree<-,TreeSummarizedExperiment-method	TreeSummarizedExperiment-accessor
rowTreeNames	TreeSummarizedExperiment-accessor
rowTreeNames,TreeSummarizedExperiment-method	TreeSummarizedExperiment-accessor
rowTreeNames<-	TreeSummarizedExperiment-accessor
rowTreeNames<-,TreeSummarizedExperiment-method	TreeSummarizedExperiment-accessor
shareNode	shareNode
showNode	showNode
signalNode	joinNode
subsetByNode	TreeSummarizedExperiment-accessor
subsetByNode,TreeSummarizedExperiment-method	TreeSummarizedExperiment-accessor
tinyTree	tinyTree
toTree	toTree
trackNode	trackNode
transNode	convertNode
TreeSummarizedExperiment	TreeSummarizedExperiment-constructor
TreeSummarizedExperiment-accessor	TreeSummarizedExperiment-accessor
TreeSummarizedExperiment-class	TreeSummarizedExperiment-class
TreeSummarizedExperiment-combine	TreeSummarizedExperiment-combine
TreeSummarizedExperiment-constructor	TreeSummarizedExperiment-constructor
TreeSummarizedExperiment-internal	TreeSummarizedExperiment-internal
unionLeaf	unionLeaf
updateObject,TreeSummarizedExperiment-method	updateObject-TreeSummarizedExperiment-method
vertical_slot_names,TreeSummarizedExperiment-method	TreeSummarizedExperiment-internal
[,TreeSummarizedExperiment,ANY,ANY,ANY-method	TreeSummarizedExperiment-accessor
[<-,TreeSummarizedExperiment,ANY,ANY,TreeSummarizedExperiment-method	TreeSummarizedExperiment-accessor
