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Welcome to the pathfindR Wiki

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 (PIN) 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, ontologies, TF target gene sets etc.) that possibly underlie the phenotype of interest.

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.

The enrichment, clustering and other methods implemented in pathfindR are described in detail in Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. Front. Genet. doi:10.3389/fgene.2019.00858.

Pages

• Installation
  • Installation via pak
  • Important Notes
  • Installation of pathfindR
• Frequently encountered issues
  • Did not find any enriched terms!
  • Error in { : task 1 failed - "cannot open the connection"
• Retrieving PIN and Gene Sets Data
  • Get PIN File
  • Get Gene Sets List
• Active-subnetwork-oriented Enrichment Documentation
  • Overview
  • All Arguments of run_pathfindR()
  • Specifying the Output Directory
  • Changing the Gene Sets Used for Enrichment Analyses
  • Filtering Enriched Terms by Adjusted-p Values
  • Changing the Protein-protein Interaction Network
  • Selecting the Active Subnetwork Search Algorithm
• Clustering Documentation
  • Hierarchical Clustering
  • Heuristic Fuzzy Multiple-linkage Partitioning
• Comparison of 2 pathfindR Results
• Enriched Term Scoring
• Visualization of Enrichment Results
  • Bubble Chart of Enrichment Results
  • Term-Gene Heatmap
  • Term-Gene Graph
  • UpSet Plot of Enriched Terms
• Visualization of Enriched Terms
• Analysis Using Custom Gene Sets
• Analysis using Non-Human Organism Data
• How to run pathfindR using Docker image