Enrichment Analysis Utilizing Active Subnetworks
Wrapper for Active Subnetwork Search + Enrichment over Single/Multiple...
Perform Active Subnetwork Search
Annotate the Affected Genes in the Provided Enriched Terms
Check Java Version
Create HTML Report of pathfindR Results
Cluster Enriched Terms
Graph Visualization of Clustered Enriched Terms
Color hsa KEGG pathway
Combine 2 pathfindR Results
Combined Results Graph
Configure Output Directory Name
Create Kappa Statistics Matrix
Perform Enrichment Analysis for a Single Gene Set
Perform Enrichment Analyses on the Input Subnetworks
Create Bubble Chart of Enrichment Results
Fetch Gene Set Objects
Obtain Java Version
Parse Active Subnetwork Search Output File and Filter the Subnetworks
Heuristic Fuzzy Multiple-linkage Partitioning of Enriched Terms
Retrieve the Requested Release of Organism-specific BioGRID PIN
Retrieve Organism-specific Gene Sets List
Retrieve Organism-specific KEGG Pathway Gene Sets
Input Testing
Check if value is a valid color
Retrieve Organism-specific MSigDB Gene Sets
Retrieve Organism-specific PIN data
Retrieve Reactome Pathway Gene Sets
Retrieve Gene Sets from GMT-format File
Hierarchical Clustering of Enriched Terms
Hypergeometric Distribution-based Hypothesis Testing
Process Input
pathfindR: A package for Enrichment Analysis Utilizing Active Subnetwo...
Plot the Heatmap of Score Matrix of Enriched Terms per Sample
Process Data frame of Protein-protein Interactions
Return The Path to Given Protein-Protein Interaction Network (PIN)
Wrapper Function for pathfindR - Active-Subnetwork-Oriented Enrichment...
Calculate Agglomerated Scores of Enriched Terms for Each Subject
Active Subnetwork Search + Enrichment Analysis Wrapper for a Single It...
Summarize Enrichment Results
Create Term-Gene Graph
Create Terms by Genes Heatmap
Create UpSet Plot of Enriched Terms
Visualize Active Subnetworks
Visualize Human KEGG Pathways
Visualize Interactions of Genes Involved in the Given Enriched Terms
Create Diagrams for Enriched Terms
Enrichment analysis enables researchers to uncover mechanisms underlying a phenotype. However, conventional methods for enrichment analysis do not take into account protein-protein interaction information, resulting in incomplete conclusions. pathfindR is a tool for enrichment analysis utilizing active subnetworks. The main function identifies active subnetworks in a protein-protein interaction network using a user-provided list of genes and associated p values. It then performs enrichment analyses on the identified subnetworks, identifying enriched terms (i.e. pathways or, more broadly, gene sets) 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>.
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