Man pages for pathfindR
Pathway Enrichment Analysis Utilizing Active Subnetworks

active_snw_searchPerform Active Subnetwork Search
annotate_pathway_DEGsAnnotate the Affected Genes in the Provided Pathways
biocarta_genesBioCarta Gene Sets
biocarta_pathwaysBioCarta Pathway Descriptions
calculate_pw_scoresCalculate Pathway Scores for Each Subject
cluster_graph_visGraph Visualization of Pathway Clustering
cluster_pathwaysCluster Pathways
create_kappa_matrixCreate Kappa Statistics Matrix
custom_resultCustom Gene Set Enrichment Results
enrichmentPerform Enrichment Analysis for a Single Gene Set
enrichment_analysesPerform Enrichment Analyses on the Input Subnetworks
enrichment_chartPlot the Bubble Chart of Enrichment Results
example_active_snwsExample Active Subnetworks
filterActiveSnwsParse Active Subnetwork Search Output File and Filter the...
fuzzy_pw_clusteringHeuristic Fuzzy Multiple-linkage Partitioning of Pathways
go_all_genesGene Ontology - All Ontology Gene Sets
go_all_pathwaysGene Ontology - All Ontology Descriptions
go_bp_genesGene Ontology - Biological Process Ontology Gene Sets
go_bp_pathwaysGene Ontology - Biological Process Ontology Descriptions
go_cc_genesGene Ontology - Cellular Component Ontology Gene Sets
go_cc_pathwaysGene Ontology - Cellular Component Ontology Descriptions
go_mf_genesGene Ontology - Molecular Function Ontology Gene Sets
go_mf_pathwaysGene Ontology - Molecular Function Ontology Descriptions
hierarchical_pw_clusteringHierarchical Clustering of Pathways
hyperg_testHypergeometic Distribution-based Hypothesis Testing
input_processingProcess Input
input_testingInput Testing
kegg_genesKEGG Gene Sets
kegg_pathwaysKEGG Pathway Descriptions
pathfindRpathfindR: A package for Pathway Enrichment Analysis...
plot_scoresPlot the Heatmap of Pathway Scores
RA_clusteredExample Output for the pathfindR Clustering Workflow -...
RA_exp_matExample Input for pathfindR - pathway z-scores
RA_inputExample Input for the pathfindR Enrichment Workflow -...
RA_outputExample Output for the pathfindR Enrichment Workflow -...
reactome_genesReactome Gene Sets
reactome_pathwaysReactome Pathway Descriptions
return_pin_pathReturn The Path to Given Protein-Protein Interaction Network...
run_pathfindRWrapper Function for pathfindR Workflow
summarize_enrichment_resultsSummarize Enrichment Results
visualize_hsa_KEGGVisualize Human KEGG Pathways
visualize_pw_interactionsVisualize Interactions of Genes Involved in the Given...
visualize_pwsCreate Pathway Diagrams
pathfindR documentation built on Nov. 20, 2018, 5:06 p.m.