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.
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.
run_pathfindR for details on the pathfindR
active-subnetwork-oriented enrichment analysis
cluster_enriched_terms for details on methods of enriched
terms clustering to define clusters of biologically-related terms
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)
term_gene_heatmap for details on visualization of the heatmap
of enriched terms by involved genes
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
UpSet_plot for details on creating an UpSet plot of the
get_pin_file for obtaining organism-specific PIN data and
get_gene_sets_list for obtaining organism-specific gene sets data