API for pcahan1/epoch
Dynamic GRN reconstruction from single cell RNA-Seq data
| Global functions | |
|---|---|
| JI_across_topregs | Man page Source code |
| add_interaction_type | Man page Source code |
| add_type | Man page Source code |
| assign_epochs | Man page Source code |
| assign_epochs_simple | Man page Source code |
| average_pagerank_ranks | Source code |
| biglist_compute_betweenness_degree | Man page Source code |
| caoGenes | Man page Source code |
| cn_extractRegsDF | Man page |
| compileDynGenes | Man page Source code |
| compile_epochs | Man page Source code |
| compute_JI_topregs | Man page Source code |
| compute_betweenness | Source code |
| compute_betweenness_degree | Man page Source code |
| compute_frobenius_distance | Man page Source code |
| compute_pagerank | Man page Source code |
| cor_and_add_action | Man page Source code |
| cross_corr | Source code |
| crossweight | Man page Source code |
| crossweight_params | Source code |
| define_epochs | Man page Source code |
| diffnet_community_detection | Man page Source code |
| dynamic_difference_network | Man page Source code |
| dynamic_reachability | Source code |
| dynamic_shortest_path | Man page Source code |
| dynamic_shortest_path_multiple | Man page Source code |
| edge_rank | Man page Source code |
| edge_uniqueness | Man page Source code |
| epochGRN | Man page Source code |
| findDynGenes | Man page Source code |
| find_communities | Man page Source code |
| find_cuts_by_clustering | Man page Source code |
| find_cuts_by_similarity | Man page Source code |
| find_paths_to | Source code |
| find_targets | Man page Source code |
| flatten_network | Source code |
| gamFit | Source code |
| get_legend | Source code |
| grnKsmooth | Man page Source code |
| heatmap_by_treatment_group | Man page Source code |
| hm_dyn | Man page Source code |
| hm_dyn_clust | Man page Source code |
| hm_dyn_epoch | Man page Source code |
| ig_exemplars | Source code |
| ig_tabToIgraph | Man page |
| loadDataFromLoom | Man page Source code |
| load_SP_effectors | Man page Source code |
| mean_module_expression | Man page Source code |
| mean_subnetwork_expression | Man page Source code |
| order_genes | Man page Source code |
| plotPairs | Source code |
| plotRegulon | Source code |
| plot_diffnet_detail | Man page Source code |
| plot_dyn_diffnet | Man page Source code |
| plot_dynamic_network | Man page Source code |
| plot_dynnet_detail | Man page Source code |
| plot_heatmap_by_treatment | Man page Source code |
| plot_reachability_community_coverage | Source code |
| plot_targets | Man page Source code |
| plot_targets_and_regulators | Man page Source code |
| plot_targets_with_top_regulators | Man page Source code |
| plot_targets_with_top_regulators_detail | Man page Source code |
| plot_top_regulators | Man page Source code |
| reconstructGRN | Man page Source code |
| reconstructGRN_GENIE3 | Man page Source code |
| rough_hierarchy | Source code |
| sample_and_epoch_reconstruct | Man page Source code |
| score_offset | Source code |
| score_targets | Man page Source code |
| split_epochs_by_group | Man page Source code |
| split_epochs_by_pseudotime | Man page Source code |
| static_reachability | Source code |
| static_shortest_path | Man page Source code |
| subnets | Man page Source code |
| tally_topregs | Source code |
| tfnet_pagerank | Man page Source code |
| utils_loadObject | Man page |
| wn_ig_tabToIgraph | Man page |
