![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| 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 |
| GO_all_terms_df | Gene Ontology - All Gene Ontology Descriptions |
| 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 |
| 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 |
| 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_terms | Create Diagrams for Enriched Terms |
| visualize_term_interactions | Visualize Interactions of Genes Involved in the Given Enriched Terms |