API for cbg-ethz/TreeMHN
Joint inference of repeated evolutionary trajectories and patterns of clonal exclusivity from single-cell mutation trees
| Global functions | |
|---|---|
| .onLoad | Source code |
| KL_divergence | Man page Source code |
| Theta_to_pathways | Man page Source code |
| Theta_to_pathways_w_sampling | Source code |
| build_poset | Source code |
| build_tr_mat | Source code |
| compare_Theta | Man page Source code |
| compatible_genotypes | Source code |
| compute_obs_ll | Source code |
| full_MHN_grad | Source code |
| full_MHN_objective | Source code |
| generate_tree_MHN | Source code |
| generate_trees | Man page Source code |
| get_MC_flags | Man page Source code |
| get_augmented_trees | Source code |
| get_children | Source code |
| get_hintra_pathways | Man page Source code |
| get_lambda | Source code |
| get_next_mutations | Source code |
| get_node_labels | Source code |
| get_observed_pathways | Source code |
| get_pathway_tree_df | Source code |
| get_pathway_tree_list | Source code |
| get_revolver_pathways | Man page Source code |
| initialize_Theta | Man page Source code |
| input_tree_df | Man page Source code |
| is_ancestor | Source code |
| learn_MHN | Man page Source code |
| obj_grad_helper | Source code |
| obs_MHN_grad | Source code |
| obs_MHN_objective | Source code |
| output_one_tree_df | Source code |
| output_tree_df | Man page Source code |
| pathway_helper | Source code |
| perturb_tree | Source code |
| perturb_trees | Source code |
| plot_Theta | Man page Source code |
| plot_next_mutations | Man page Source code |
| plot_observed_pathways | Man page Source code |
| plot_pathways | Man page Source code |
| plot_pathways_w_sampling | Man page Source code |
| plot_tree_df | Man page Source code |
| plot_tree_list | Man page Source code |
| random_Theta | Man page Source code |
| remove_duplicates | Source code |
| sort_one_tree_df | Man page Source code |
| transitive_closure | Source code |
| tree_df_to_genotypes | Man page Source code |
| tree_df_to_trees | Man page Source code |
| trees_to_revolver_W | Man page Source code |
| update_timed_trees | Source code |
