UpSet_plot              Create UpSet Plot of Enriched Terms
active_snw_enrichment_wrapper
                        Wrapper for Active Subnetwork Search +
                        Enrichment over Single/Multiple Iteration(s)
active_snw_search       Perform Active Subnetwork Search
annotate_term_genes     Annotate the Affected Genes in the Provided
                        Enriched Terms
check_java_version      Check Java Version
cluster_enriched_terms
                        Cluster Enriched Terms
cluster_graph_vis       Graph Visualization of Clustered Enriched Terms
color_kegg_pathway      Color hsa KEGG pathway
combine_pathfindR_results
                        Combine 2 pathfindR Results
combined_results_graph
                        Combined Results Graph
configure_output_dir    Configure Output Directory Name
create_HTML_report      Create HTML Report of pathfindR Results
create_kappa_matrix     Create Kappa Statistics Matrix
enrichment              Perform Enrichment Analysis for a Single Gene
                        Set
enrichment_analyses     Perform Enrichment Analyses on the Input
                        Subnetworks
enrichment_chart        Create Bubble Chart of Enrichment Results
fetch_gene_set          Fetch Gene Set Objects
fetch_java_version      Obtain Java Version
filterActiveSnws        Parse Active Subnetwork Search Output File and
                        Filter the Subnetworks
fuzzy_term_clustering   Heuristic Fuzzy Multiple-linkage Partitioning
                        of Enriched Terms
get_biogrid_pin         Retrieve the Requested Release of
                        Organism-specific BioGRID PIN
get_gene_sets_list      Retrieve Organism-specific Gene Sets List
get_kegg_gsets          Retrieve Organism-specific KEGG Pathway Gene
                        Sets
get_mgsigdb_gsets       Retrieve Organism-specific MSigDB Gene Sets
get_pin_file            Retrieve Organism-specific PIN data
get_reactome_gsets      Retrieve Reactome Pathway Gene Sets
gset_list_from_gmt      Retrieve Gene Sets from GMT-format File
hierarchical_term_clustering
                        Hierarchical Clustering of Enriched Terms
hyperg_test             Hypergeometric Distribution-based Hypothesis
                        Testing
input_processing        Process Input
input_testing           Input Testing
isColor                 Check if value is a valid color
pathfindR               pathfindR: A package for Enrichment Analysis
                        Utilizing Active Subnetworks
plot_scores             Plot the Heatmap of Score Matrix of Enriched
                        Terms per Sample
process_pin             Process Data frame of Protein-protein
                        Interactions
return_pin_path         Return The Path to Given Protein-Protein
                        Interaction Network (PIN)
run_pathfindR           Wrapper Function for pathfindR -
                        Active-Subnetwork-Oriented Enrichment Workflow
safe_get_content        Safely download and parse web content
score_terms             Calculate Agglomerated Scores of Enriched Terms
                        for Each Subject
single_iter_wrapper     Active Subnetwork Search + Enrichment Analysis
                        Wrapper for a Single Iteration
summarize_enrichment_results
                        Summarize Enrichment Results
term_gene_graph         Create Term-Gene Graph
term_gene_heatmap       Create Terms by Genes Heatmap
visualize_KEGG_diagram
                        Visualize Human KEGG Pathways
visualize_active_subnetworks
                        Visualize Active Subnetworks
visualize_term_interactions
                        Visualize Interactions of Genes Involved in the
                        Given Enriched Terms
visualize_terms         Create Diagrams for Enriched Terms
