# Pathway Enrichment Analysis Utilizing Active Subnetworks

## Documentation for package ‘pathfindR’ version 1.3.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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