Man pages for pathfindR
Enrichment Analysis Utilizing Active Subnetworks

active_snw_searchPerform Active Subnetwork Search
annotate_term_genesAnnotate the Affected Genes in the Provided Enriched Terms
check_java_versionCheck Java Version
cluster_enriched_termsCluster Enriched Terms
cluster_graph_visGraph Visualization of Clustered Enriched Terms
color_kegg_pathwayColor hsa KEGG pathway
combined_results_graphCombined Results Graph
combine_pathfindR_resultsCombine 2 pathfindR Results
create_kappa_matrixCreate Kappa Statistics Matrix
download_kegg_pngDownload Colored KEGG Diagram PNG
enrichmentPerform Enrichment Analysis for a Single Gene Set
enrichment_analysesPerform Enrichment Analyses on the Input Subnetworks
enrichment_chartCreate Bubble Chart of Enrichment Results
fetch_gene_setFetch Gene Set Objects
fetch_java_versionObtain Java Version
filterActiveSnwsParse Active Subnetwork Search Output File and Filter the...
fuzzy_term_clusteringHeuristic Fuzzy Multiple-linkage Partitioning of Enriched...
get_biogrid_pinRetrieve the Requested Release of Organism-specific BioGRID...
get_gene_sets_listRetrieve Organism-specific Gene Sets List
get_kegg_gsetsRetrieve Organism-specific KEGG Pathway Gene Sets
get_mgsigdb_gsetsRetrieve Organism-specific MSigDB Gene Sets
get_pin_fileRetrieve Organism-specific PIN data
get_reactome_gsetsRetrieve Reactome Pathway Gene Sets
gset_list_from_gmtRetrieve Gene Sets from GMT-format File
hierarchical_term_clusteringHierarchical Clustering of Enriched Terms
hyperg_testHypergeometric Distribution-based Hypothesis Testing
input_processingProcess Input
input_testingInput Testing
obtain_colored_urlObtain URL for a KEGG pathway diagram with a given set of...
obtain_KEGGML_URLObtain KGML file for a KEGG pathway (hsa)
pathfindRpathfindR: A package for Enrichment Analysis Utilizing Active...
plot_scoresPlot the Heatmap of Score Matrix of Enriched Terms per Sample
process_pinProcess Data frame of Protein-protein Interactions
return_pin_pathReturn The Path to Given Protein-Protein Interaction Network...
run_pathfindRWrapper Function for pathfindR - Active-Subnetwork-Oriented...
score_termsCalculate Agglomerated Scores of Enriched Terms for Each...
summarize_enrichment_resultsSummarize Enrichment Results
term_gene_graphCreate Term-Gene Graph
term_gene_heatmapCreate Terms by Genes Heatmap
UpSet_plotCreate UpSet Plot of Enriched Terms
visualize_active_subnetworksVisualize Active Subnetworks
visualize_hsa_KEGGVisualize Human KEGG Pathways
visualize_term_interactionsVisualize Interactions of Genes Involved in the Given...
visualize_termsCreate Diagrams for Enriched Terms
pathfindR documentation built on Nov. 15, 2021, 5:06 p.m.