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| pathfindR-package | pathfindR: A package for Pathway Enrichment Analysis Utilizing Active Subnetworks |
| 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 |
| 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 |
| 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_pws | Create Pathway Diagrams |
| visualize_pw_interactions | Visualize Interactions of Genes Involved in the Given Pathways |