Enrichment Analysis Utilizing Active Subnetworks

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Documentation for package ‘pathfindR’ version 2.3.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

pathfindR-package	pathfindR: A package for Enrichment Analysis Utilizing Active Subnetworks
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
download_KGML_file	Obtain KGML file for a KEGG pathway (hsa)
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
isColor	Check if value is a valid color
obtain_colored_url	Obtain URL for a KEGG pathway diagram with a given set of genes marked
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
single_iter_wrapper	Active Subnetwork Search + Enrichment Analysis Wrapper for a Single Iteration
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