# Enrichment Analysis Utilizing Active Subnetworks

## Documentation for package ‘pathfindR’ version 2.0.1

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

## Help Pages

active_snw_enrichment_wrapper | Wrapper for Active Subnetwork Search + Enrichment over Single/Multiple Iteration(s)
active_snw_search | Perform Active Subnetwork Search
annotate_term_genes | Annotate the Affected Genes in the Provided Enriched Terms
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
combined_results_graph | Combined Results Graph
combine_pathfindR_results | Combine 2 pathfindR Results
configure_output_dir | Configure Output Directory Name
create_HTML_report | Create HTML Report of pathfindR Results
create_kappa_matrix | Create Kappa Statistics Matrix
download_kegg_png | Download Colored KEGG Diagram PNG
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
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
get_biogrid_pin | Retrieve the Requested Release of Organism-specific BioGRID PIN
get_gene_sets_list | Retrieve Organism-specific Gene Sets List
get_kegg_gsets | Retrieve Organism-specific KEGG Pathway Gene Sets
get_mgsigdb_gsets | Retrieve Organism-specific MSigDB Gene Sets
get_pin_file | Retrieve Organism-specific PIN data
get_reactome_gsets | Retrieve Reactome Pathway Gene Sets
gset_list_from_gmt | Retrieve Gene Sets from GMT-format File
hierarchical_term_clustering | Hierarchical Clustering of Enriched Terms
hyperg_test | Hypergeometric Distribution-based Hypothesis Testing
input_processing | Process Input
input_testing | Input Testing
obtain_colored_url | Obtain URL for a KEGG pathway diagram with a given set of genes marked
obtain_KEGGML_URL | Obtain KGML file for a KEGG pathway (hsa)
pathfindR | pathfindR: A package for Enrichment Analysis Utilizing Active Subnetworks
plot_scores | Plot the Heatmap of Score Matrix of Enriched Terms per Sample
process_pin | Process Data frame of Protein-protein Interactions
return_pin_path | Return The Path to Given Protein-Protein Interaction Network (PIN)
run_pathfindR | Wrapper Function for pathfindR - Active-Subnetwork-Oriented Enrichment Workflow
score_terms | Calculate Agglomerated Scores of Enriched Terms for Each Subject
summarize_enrichment_results | Summarize Enrichment Results
term_gene_graph | Create Term-Gene Graph
term_gene_heatmap | Create Terms by Genes Heatmap
UpSet_plot | Create UpSet Plot of Enriched Terms
visualize_active_subnetworks | Visualize Active Subnetworks
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