# Enrichment Analysis Utilizing Active Subnetworks

## Documentation for package ‘pathfindR’ version 1.4.2

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

## Help Pages

active_snw_search | Perform Active Subnetwork Search
annotate_term_genes | Annotate the Affected Genes in the Provided Enriched Terms
biocarta_descriptions | BioCarta Pathways - Descriptions
biocarta_genes | BioCarta Pathways - Gene Sets
biogrid_adj_list | BioGRID PIN Adjacency List
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
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 | Create Bubble Chart of Enrichment Results
example_active_snws | Example Active Subnetworks
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
genemania_adj_list | GeneMania PIN Adjacency List
go_all_genes | Gene Ontology - All Gene Ontology Gene Sets
GO_all_terms_df | Gene Ontology - All Gene Ontology Descriptions
hierarchical_term_clustering | Hierarchical Clustering of Enriched Terms
hyperg_test | Hypergeometric Distribution-based Hypothesis Testing
input_processing | Process Input
input_testing | Input Testing
intact_adj_list | IntAct PIN Adjacency List
kegg_adj_list | KEGG PIN Adjacency List
kegg_descriptions | KEGG Pathways - Descriptions
kegg_genes | KEGG Pathways - Gene Sets
mmu_kegg_descriptions | Mus Musculus KEGG Pathways - Descriptions
mmu_kegg_genes | Mus Musculus KEGG Pathways - Gene Sets
mmu_string_adj_list | Mus musculus STRING PIN Adjacency List
myeloma_input | Example Input for Myeloma Analysis (Mus Musculus)
myeloma_output | Example Output for Myeloma Analysis (Mus Musculus)
pathfindR | pathfindR: A package for Enrichment Analysis Utilizing Active Subnetworks
plot_scores | Plot the Heatmap of Score Matrix of Enriched Terms per Sample
RA_clustered | Example Output for the pathfindR Clustering Workflow - Rheumatoid Arthritis
RA_exp_mat | Example Input for pathfindR - Enriched Term Scoring
RA_input | Example Input for the pathfindR Enrichment Workflow - Rheumatoid Arthritis
RA_output | Example Output for the pathfindR Enrichment Workflow - Rheumatoid Arthritis
reactome_descriptions | Reactome Pathways - Descriptions
reactome_genes | Reactome Pathways - Gene Sets
return_pin_path | Return The Path to Given Protein-Protein Interaction Network (PIN)
run_pathfindR | Wrapper Function for pathfindR - Active-Subnetwork-Oriented Enrichment Analysis
score_terms | Calculate Agglomerated Scores of Enriched Terms for Each Subject
string_adj_list | STRING PIN Adjacency List
summarize_enrichment_results | Summarize Enrichment Results
term_gene_graph | Plot Term-Gene Graph
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