add_expression          attach expression values from user-provided
                        expression vector to graph.
add_value               Attach a generic user-provided value to graph
as_gene_symbol          Convert from most other representations of gene
                        name to gene.symbol
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 in a user-provided vector - cpp
                        internal version
calc_np_all_legacy      function to calculate the network potential for
                        each protein in a user-provided vector
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 relationship to user-provided
                        seeds.
compute_dnp             main function to compute delta np for every
                        gene in a given dataframe - assumes compute_np
                        has already been run for a given dataset
compute_np              main function to compute np from a
                        user-provided expression matrix.
compute_null_dnp        function to compute null distribution of dnp
crosstalk_subgraph      Helper function to generate subgraph from
                        crosstalk_df output of 'compute_crosstalk'
crosstalkr              crosstalkr: A package for the identification of
                        functionally relevant subnetworks from
                        high-dimensional omics data.
detect_inputtype        Determine which format of gene is used to
                        specify by user-defined seed proteins
dist_calc               Internal function that computes the mean/stdev
                        for each gene from a wide-format data frame.
ensembl_type            Determine if ensembl id is a Protein, gene, or
                        transcript_id
experiment_breakout     helper function to split experiment names into
                        constituent parts
fcalc_np_all            Function to calculate the network potential for
                        vertices v
final_combine           final .combine function to run in
                        compute_null_dnp foreach looping structure
final_dist_calc         Internal function that computes the mean/stdev
                        for each gene from a wide-format data frame.
get_neighbors           function to get graph neighbors (along with
                        their expression values) for a given gene in a
                        given network g
get_random_graph        Helper function for compute_null_dnp - returns
                        a graph with randomly permuted edges.
get_topn                Helper function for compute_null_dnp - returns
                        the top n genes by dnp for each sample
gfilter                 Generic function to filter either an igraph
                        object or a PPI network
gfilter.ct              Method to filter the graph based on parameters
                        passed to compute_crosstalk
gfilter.igraph_method   Method to filter graph based on any igraph
                        method that scores verticies.
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 distribution to parent seed proteins
node_repression         Function to eliminate a node from a network g
                        and calculate the change in some measure of
                        network state
norm_colsum             Function to normalize adjacency matrix by
                        dividing each value by the colsum.
plot_ct                 Plot subnetwork identified using the
                        compute_crosstalk function
ppi_intersection        Function to allow users to choose the
                        intersection of stringdb and biogrid Only works
                        with the human PPI. min_score parameter only
                        applies to strindb
ppi_union               Function to allow users to choose the union of
                        stringdb and biogrid Only works with the human
                        PPI. min_score parameter only applies to
                        strindb
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 dataframe (if not already)
to_taxon_id             helper to convert user-inputs to ncbi reference
                        taxonomy.
