Man pages for NCBI-Hackathons/robustSingleCell
Robust Subpopulation dEcision Trees
| align | Align two binary ordered trees |
| as_binary_tree | Generic method for convert trees to binary tree |
| as_binary_tree.default | Convert a newick string as a binary tree object |
| as_binary_tree.hclust | Convert a hclust object as a binary tree object |
| as_binary_tree.phylo | Convert a phylo object as a binary tree object |
| as_phylo | Convert a binary tree as phylo object |
| binary_tree | Create a binary tree object |
| clustertree_construction | Construct clustering tree from proportion graph |
| construct_hierarchy | Construct Hierarchy based on Cluster Mean |
| cost_matrix | Create cost matrix based on distance |
| create_align_object | Create alignment object |
| DE_level_k | sensitive DE at level k of the hierarchy |
| fill_matrix | Fill T matrix and F map |
| get_HVG | Get highly variable genes |
| get_jaccard | return the pairwise Jaccard coefficients between two... |
| initialize | Intialize the T matrix and F map |
| PhenoGraphVarRes | PhenoGraph Clustering with Various Resolution |
| plot.binary_tree | Plot binary tree |
| plot_graph | Plot a igraph object |
| plot.hierarchy | Plot Hierarchy Constructed |
| postorder_labels | Get labels by postorder traversal |
| preprocess_data | Preprocess 10X dataset |
| sens_DE | sensitive DE at all levels of the hierarchy |
| sensDE_limma | Use limma to find differentially expressed genes |
| SimpleDE | Differential expression that iteratively compares one cluster... |
| test_alignment_configuration | Test alignment method |
| test_hierarchy_construction | Test hierarchy construction |
| traceback | Traceback for constructing aligned tree |
