LinkDataFrame-class     LinkDataFrame: A S4 class extended from
                        DataFrame An S4 class LinkDataFrame
LinkDataFrame-constructor
                        Construct a LinkDataFrame Construct a
                        LinkDataFrame object
TreeSummarizedExperiment-class
                        An S4 class TreeSummarizedExperiment
TreeSummarizedExperiment-constructor
                        Construct a TreeSummarizedExperiment object
TreeeSummarizedExperiment-package
                        The 'TreeSummarizedExperiment' package
addLabel                add labels to nodes of a tree
aggTSE                  Perform data aggregations based on the
                        available tree structures
aggValue                Perform data aggregations based on the
                        available tree structures
asLeaf                  change internal nodes to leaf nodes
asPhylo                 Convert a data frame to a phylo object
changeTree              Change the row or column tree
countLeaf               count the number of leaf nodes
countNode               count the number of nodes
detectLoop              Detect loops 'detectLoop' detects loops
distNode                Calculate the distance between any two nodes on
                        the tree
findAncestor            Find the ancestors of specified nodes
findChild               Find the children
findOS                  Find descendants (or offsprings)
findSibling             find the sibling node
isLeaf                  To test whether the specified nodes are leaf
                        nodes
makeTSE                 A toy TreeSummarizedExperiment object
matTree                 Transform a phylo object into a matrix.
printNode               To print out the node labels
rbind,TreeSummarizedExperiment-method
                        Combine TSEs by rows or columns
resolveLoop             Resolve loops 'resolveLoop' resolve loops by
                        adding suffix to the child node. The suffix is
                        "_i" where 'i' is a number. Please see
                        examples.
rowLinks                TreeSummarizedExperiment-accessors
shareNode               Find the share node
showNode                Find nodes on the tree
signalNode              Join nodes
tinyTree                A simulated phylogenetic tree with 10 tips and
                        9 internal nodes
toTree                  Translate a data frame to a phylo object
trackNode               track the nodes of a phylo tree
transNode               Transfer between node number and node label
unionLeaf               list leaf nodes that are the descendants of at
                        least one specified node
updateObject,TreeSummarizedExperiment-method
                        Update a 'TreeSummarizedExperiment' object
