Man pages for fionarhuang/treeclimbR
An algorithm to find optimal signal levels in a tree
| aggDS | Aggregate observed data based on a tree |
| 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... |
| 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... |
| 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 |
| treeclimbR-package | treeclimbR |
| TreeHeatmap | Generate a heatmap corresponding to an arbitrary aggregation... |
| treeScore | Generate weighted tree score accounting for the family effect |
