pathfindR is a tool for active-subnetwork-oriented gene set enrichment analysis. The main aim of the package is to identify active subnetworks in a protein-protein interaction network using a user-provided list of genes and associated p values then performing enrichment analyses on the identified subnetworks, discovering enriched terms (i.e. pathways, gene ontology, TF target gene sets etc.) that possibly underlie the phenotype of interest.

## Details

For analysis on non-Homo sapiens organisms, pathfindR offers utility functions for obtaining organism-specific PIN data and organism-specific gene sets data.

pathfindR also offers functionalities to cluster the enriched terms and identify representative terms in each cluster, to score the enriched terms per sample and to visualize analysis results.

See run_pathfindR for details on the pathfindR active-subnetwork-oriented enrichment analysis See cluster_enriched_terms for details on methods of enriched terms clustering to define clusters of biologically-related terms See score_terms for details on agglomerated score calculation for enriched terms to investigate how a gene set is altered in a given sample (or in cases vs. controls) See term_gene_heatmap for details on visualization of the heatmap of enriched terms by involved genes See term_gene_graph for details on visualizing terms and term-related genes as a graph to determine the degree of overlap between the enriched terms by identifying shared and/or distinct significant genes See UpSet_plot for details on creating an UpSet plot of the enriched terms. See get_pin_file for obtaining organism-specific PIN data and get_gene_sets_list for obtaining organism-specific gene sets data