Package index • treeclimbR

All functions
`TreeHeatmap()`	Generate a heatmap corresponding to an arbitrary aggregation level of a tree
`aggDS()`	Aggregate observed data based on a tree
`buildTree()` `calcMediansByTreeMarker()` `calcTreeCounts()` `calcTreeMedians()`	Tree versions of diffcyt functions
`edgerWrp()`	Wrapper applying an edgeR differential analysis workflow
`evalCand()`	Evaluate candidate levels and select the optimal one
`fdr()`	Calculate false discovery rate (FDR) on a tree structure
`findChild()`	Find the children of an internal node in a tree
`findExcl()`	Find branches that are non-overlapping with specified branches in a tree
`getCand()`	Generate candidates for different thresholds
`getData()`	Extract data from a TreeHeatmap
`getLevel()`	Search for a target level on the tree via a specified score
`infoCand()`	Get information of candidates
`isConnect()`	Check whether nodes are contained in the same path from a leaf to the root in a tree
`medianByClusterMarker()`	Calculate median values of markers for each cluster
`nodeResult()`	Extract table with node-level DA/DS results
`parEstimate()`	Parameter estimation for Dirichlet-multinomial distribution
`runDA()`	Test for differential abundance using edgeR
`runDS()`	Test for differential state using edgeR
`selNode()`	Select branches meeting certain criteria
`simData()`	Simulate different scenarios of abundance change in entities
`topNodes()`	Generate a table of top-ranked entities (nodes)
`tpr()`	Calculate true positive rate (TPR) on a tree structure
`treeScore()`	Generate weighted tree score accounting for the family effect

Reference

All functions