Man pages for pcahan1/epoch
Dynamic GRN reconstruction from single cell RNA-Seq data
| add_interaction_type | Add interaction type to static or dynamic GRN |
| add_type | Adds interaction type to dynamic differential network |
| assign_epochs | Assigns genes to epochs |
| assign_epochs_simple | Assigns genes to epochs just based on which mean is maximal |
| biglist_compute_betweenness_degree | Computes betweenness and degree of each TF for each network... |
| caoGenes | cluster and order genes |
| cn_extractRegsDF | Create GRN table |
| compileDynGenes | compiles results from findDynGenes run on separate paths |
| compile_epochs | compile epochs on branched trajectories |
| compute_betweenness_degree | Function to compute betweenness and degree |
| compute_frobenius_distance | Computes frobenius distance in a pairwise manner between two... |
| compute_JI_topregs | Computes Jaccard similarity between top regulators in two... |
| compute_pagerank | Function to compute page rank of TF+target networks |
| cor_and_add_action | Adds an extra column to the result of... |
| crossweight | Perform crossweighting |
| define_epochs | Define epochs |
| diffnet_community_detection | Perform community detection on a dynamic network |
| dynamic_difference_network | Compute a dynamic difference network |
| dynamic_shortest_path | Function to return shortest path from 1 TF to 1 TG in a... |
| dynamic_shortest_path_multiple | Function to return shortest path from multiple TFs to... |
| edge_rank | Function to compute edge differences |
| edge_uniqueness | Function to compute edge differences between networks |
| epochGRN | Divides grnDF into epochs, filters interactions between genes... |
| find_communities | Find communities in a static or dynamic network |
| find_cuts_by_clustering | Returns cuts to define epochs |
| find_cuts_by_similarity | Returns cuts to define epochs |
| findDynGenes | find genes expressed dynamically |
| find_targets | Finds binding targets given list of dataframes containing... |
| grnKsmooth | smooths expression |
| heatmap_by_treatment_group | Useful plotting function to plot heatmap of module expression... |
| hm_dyn | plots results of findDynGenes |
| hm_dyn_clust | plots results of findDynGenes |
| hm_dyn_epoch | heatmap |
| ig_tabToIgraph | convert a table to an igraph |
| JI_across_topregs | Computes Jaccard similarity between top regulators in two... |
| loadDataFromLoom | Loads .obs and .var data from loom file |
| load_SP_effectors | Function to load in tsv files from Chip-Atlas |
| mean_module_expression | Computes mean expression of groups of genes |
| mean_subnetwork_expression | Computes mean expression of groups of genes in a dynamic... |
| order_genes | Function that orders genes based on peak expression |
| plot_diffnet_detail | Plot the dynamic differential network but colored by... |
| plot_dynamic_network | quick plot of dynamic networks |
| plot_dyn_diffnet | Plot the dynamic differential network |
| plot_dynnet_detail | Plot the dynamic differential network but colored by... |
| plot_heatmap_by_treatment | Useful plotting function to plot heatmap with pre-split expX |
| plot_targets | quick plot of top targets of specified regulators |
| plot_targets_and_regulators | Updated plot of top regulators given targets in dynamic... |
| plot_targets_with_top_regulators | quick plot of top regulators given targets in dynamic... |
| plot_targets_with_top_regulators_detail | quick plot of top regulators given targets in dynamic... |
| plot_top_regulators | quick plot of top regulators in dynamic networks |
| reconstructGRN | reconstruct GRN ala CLR |
| reconstructGRN_GENIE3 | reconstruct GRN ala GENIE3 |
| sample_and_epoch_reconstruct | Function to bootstrap Epoch reconstruction |
| score_targets | Function to score targets of effectors |
| split_epochs_by_group | Splits data into epochs manually |
| split_epochs_by_pseudotime | Splits data into epochs |
| static_shortest_path | Function to return shortest path from 1 TF to 1 TG in a... |
| subnets | Function to assign nodes to communities via Louvain... |
| tfnet_pagerank | Function to compute page rank of TF-only networks |
| utils_loadObject | loads an R object when you don't know the name |
| wn_ig_tabToIgraph | convert a table to an igraph |
