| add_expression | attach expression values from user-provided expression vector... |
| add_value | Attach a generic user-provided value to graph |
| as_gene_symbol | Convert from most other representations of gene name to... |
| bootstrap_null | Bootstrap null distribution for RWR |
| calc_dnp_i | helper function to calculate dnp for one sample |
| calc_np | calculate network potential for one node. |
| calc_np_all | function to calculate the network potential for each protein... |
| calc_np_all_legacy | function to calculate the network potential for each protein... |
| calc_np_i | helper function to calculate np for one sample |
| check_crosstalk | Check to make sure incoming object is a valid crosstalk df. |
| combine_null | .combine function for compute_null foreach looping structure |
| compute_crosstalk | Identify proteins with a statistically significant... |
| compute_dnp | main function to compute delta np for every gene in a given... |
| compute_np | main function to compute np from a user-provided expression... |
| compute_null_dnp | function to compute null distribution of dnp |
| crosstalkr | crosstalkr: A package for the identification of functionally... |
| crosstalk_subgraph | Helper function to generate subgraph from crosstalk_df output... |
| detect_inputtype | Determine which format of gene is used to specify by... |
| dist_calc | Internal function that computes the mean/stdev for each gene... |
| ensembl_type | Determine if ensembl id is a Protein, gene, or transcript_id |
| experiment_breakout | helper function to split experiment names into constituent... |
| fcalc_np_all | Function to calculate the network potential for vertices v |
| final_combine | final .combine function to run in compute_null_dnp foreach... |
| final_dist_calc | Internal function that computes the mean/stdev for each gene... |
| get_neighbors | function to get graph neighbors (along with their expression... |
| get_random_graph | Helper function for compute_null_dnp - returns a graph with... |
| get_topn | Helper function for compute_null_dnp - returns the top n... |
| gfilter | Generic function to filter either an igraph object or a PPI... |
| gfilter.ct | Method to filter the graph based on parameters passed to... |
| gfilter.igraph_method | Method to filter graph based on any igraph method that scores... |
| gfilter.np | Method to filter graph based on network potential values. |
| gfilter.value | Method to filter graph based on user provided value |
| is_ensembl | Determine if a character vector contains ensembl gene_ids |
| is_entrez | Determine if a character vector contains entrez gene_ids |
| load_ppi | Helper function to load requested PPI w/ parameters |
| match_seeds | Identify random sets of seeds with similar degree... |
| node_repression | Function to eliminate a node from a network g and calculate... |
| norm_colsum | Function to normalize adjacency matrix by dividing each value... |
| plot_ct | Plot subnetwork identified using the compute_crosstalk... |
| ppi_intersection | Function to allow users to choose the intersection of... |
| ppi_union | Function to allow users to choose the union of stringdb and... |
| prep_biogrid | Prepare biogrid for use in analyses |
| prep_stringdb | Prepare Stringdb for use in analyses |
| sparseRWR | Perform random walk with repeats on a sparse matrix |
| supported_species | returns a dataframe with information on supported species |
| tidy_expression | helper function to convert expression matrix to tidy... |
| to_taxon_id | helper to convert user-inputs to ncbi reference taxonomy. |
