R: An algorithm to find optimal signal levels in a tree

# An algorithm to find optimal signal levels in a tree

## Documentation for package ‘treeclimbR’ version 1.9.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

aggDS | Aggregate observed data based on a tree
buildTree | Tree versions of diffcyt functions
calcMediansByTreeMarker | Tree versions of diffcyt functions
calcTreeCounts | Tree versions of diffcyt functions
calcTreeMedians | Tree versions of diffcyt functions
diffcyt_workflow | 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
TreeHeatmap | Generate a heatmap corresponding to an arbitrary aggregation level of a tree
treeScore | Generate weighted tree score accounting for the family effect