GO_all_terms_df         Gene Ontology - All Gene Ontology Descriptions
RA_clustered            Example Output for the pathfindR Clustering
                        Workflow - Rheumatoid Arthritis
RA_exp_mat              Example Input for pathfindR - Enriched Term
                        Scoring
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_term_genes     Annotate the Affected Genes in the Provided
                        Enriched Terms
biocarta_descriptions   BioCarta Pathways - Descriptions
biocarta_genes          BioCarta Pathways - Gene Sets
biogrid_adj_list        BioGRID PIN Adjacency List
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
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        Create Bubble Chart of Enrichment Results
example_active_snws     Example Active Subnetworks
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
genemania_adj_list      GeneMania PIN Adjacency List
go_all_genes            Gene Ontology - All Gene Ontology Gene Sets
hierarchical_term_clustering
                        Hierarchical Clustering of Enriched Terms
hyperg_test             Hypergeometric Distribution-based Hypothesis
                        Testing
input_processing        Process Input
input_testing           Input Testing
intact_adj_list         IntAct PIN Adjacency List
kegg_adj_list           KEGG PIN Adjacency List
kegg_descriptions       KEGG Pathways - Descriptions
kegg_genes              KEGG Pathways - Gene Sets
mmu_kegg_descriptions   Mus Musculus KEGG Pathways - Descriptions
mmu_kegg_genes          Mus Musculus KEGG Pathways - Gene Sets
mmu_string_adj_list     Mus musculus STRING PIN Adjacency List
myeloma_input           Example Input for Myeloma Analysis (Mus
                        Musculus)
myeloma_output          Example Output for Myeloma Analysis (Mus
                        Musculus)
pathfindR               pathfindR: A package for Enrichment Analysis
                        Utilizing Active Subnetworks
plot_scores             Plot the Heatmap of Score Matrix of Enriched
                        Terms per Sample
reactome_descriptions   Reactome Pathways - Descriptions
reactome_genes          Reactome Pathways - Gene Sets
return_pin_path         Return The Path to Given Protein-Protein
                        Interaction Network (PIN)
run_pathfindR           Wrapper Function for pathfindR -
                        Active-Subnetwork-Oriented Enrichment Analysis
score_terms             Calculate Agglomerated Scores of Enriched Terms
                        for Each Subject
string_adj_list         STRING PIN Adjacency List
summarize_enrichment_results
                        Summarize Enrichment Results
term_gene_graph         Plot Term-Gene Graph
visualize_hsa_KEGG      Visualize Human KEGG Pathways
visualize_term_interactions
                        Visualize Interactions of Genes Involved in the
                        Given Enriched Terms
visualize_terms         Create Diagrams for Enriched Terms
