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 |