Pathway Enrichment Analysis Utilizing Active Subnetworks


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Documentation for package ‘pathfindR’ version 1.3.0

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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