RA_clustered            Example Output for the pathfindR Clustering
                        Workflow - Rheumatoid Arthritis
RA_exp_mat              Example Input for pathfindR - pathway z-scores
RA_input                Example Input for the pathfindR Enrichment
                        Workflow - Rheumatoid Arthritis
RA_output               Example Output for the pathfindR Enrichment
                        Workflow - Rheumatoid Arthritis
active_snw_search       Perform Active Subnetwork Search
annotate_pathway_DEGs   Annotate the Affected Genes in the Provided
                        Pathways
biocarta_genes          BioCarta Gene Sets
biocarta_pathways       BioCarta Pathway Descriptions
calculate_pw_scores     Calculate Pathway Scores for Each Subject
cluster_graph_vis       Graph Visualization of Pathway Clustering
cluster_pathways        Cluster Pathways
create_kappa_matrix     Create Kappa Statistics Matrix
custom_result           Custom Gene Set Enrichment Results
enrichment              Perform Enrichment Analysis for a Single Gene
                        Set
enrichment_analyses     Perform Enrichment Analyses on the Input
                        Subnetworks
enrichment_chart        Plot the Bubble Chart of Enrichment Results
example_active_snws     Example Active Subnetworks
filterActiveSnws        Parse Active Subnetwork Search Output File and
                        Filter the Subnetworks
fuzzy_pw_clustering     Heuristic Fuzzy Multiple-linkage Partitioning
                        of Pathways
go_all_genes            Gene Ontology - All Ontology Gene Sets
go_all_pathways         Gene Ontology - All Ontology Descriptions
go_bp_genes             Gene Ontology - Biological Process Ontology
                        Gene Sets
go_bp_pathways          Gene Ontology - Biological Process Ontology
                        Descriptions
go_cc_genes             Gene Ontology - Cellular Component Ontology
                        Gene Sets
go_cc_pathways          Gene Ontology - Cellular Component Ontology
                        Descriptions
go_mf_genes             Gene Ontology - Molecular Function Ontology
                        Gene Sets
go_mf_pathways          Gene Ontology - Molecular Function Ontology
                        Descriptions
hierarchical_pw_clustering
                        Hierarchical Clustering of Pathways
hyperg_test             Hypergeometic Distribution-based Hypothesis
                        Testing
input_processing        Process Input
input_testing           Input Testing
kegg_genes              KEGG Gene Sets
kegg_pathways           KEGG Pathway Descriptions
pathfindR               pathfindR: A package for Pathway Enrichment
                        Analysis Utilizing Active Subnetworks
plot_scores             Plot the Heatmap of Pathway Scores
reactome_genes          Reactome Gene Sets
reactome_pathways       Reactome Pathway Descriptions
return_pin_path         Return The Path to Given Protein-Protein
                        Interaction Network (PIN)
run_pathfindR           Wrapper Function for pathfindR Workflow
summarize_enrichment_results
                        Summarize Enrichment Results
visualize_hsa_KEGG      Visualize Human KEGG Pathways
visualize_pw_interactions
                        Visualize Interactions of Genes Involved in the
                        Given Pathways
visualize_pws           Create Pathway Diagrams
