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 |
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 |
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_KEGG_diagram |
Visualize Human KEGG Pathways |
visualize_terms |
Create Diagrams for Enriched Terms |
visualize_term_interactions |
Visualize Interactions of Genes Involved in the Given Enriched Terms |