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pathfindR (version 1.3.0)

Pathway Enrichment Analysis Utilizing Active Subnetworks

Description

Pathway enrichment analysis enables researchers to uncover mechanisms underlying the phenotype. pathfindR is a tool for pathway enrichment analysis utilizing active subnetworks. It identifies active subnetworks in a protein-protein interaction network using user-provided a list of genes. It performs pathway enrichment analyses on the identified subnetworks. pathfindR also offers functionalities to cluster enriched pathways and identify representative pathways and to score the pathways per sample. The method is described in detail in Ulgen E, Ozisik O, Sezerman OU. 2018. pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks. bioRxiv. .

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Install

install.packages('pathfindR')

Monthly Downloads

1,668

Version

1.3.0

License

MIT + file LICENSE

Issues

0

Pull Requests

1

Stars

188

Forks

27

Maintainer

Ege Ulgen

Last Published

November 20th, 2018

Functions in pathfindR (1.3.0)

active_snw_search

Perform Active Subnetwork Search
annotate_pathway_DEGs

Annotate the Affected Genes in the Provided Pathways
enrichment_analyses

Perform Enrichment Analyses on the Input Subnetworks
enrichment_chart

Plot the Bubble Chart of Enrichment Results
go_all_pathways

Gene Ontology - All Ontology Descriptions
go_bp_genes

Gene Ontology - Biological Process Ontology Gene Sets
input_testing

Input Testing
kegg_genes

KEGG Gene Sets
visualize_hsa_KEGG

Visualize Human KEGG Pathways
visualize_pw_interactions

Visualize Interactions of Genes Involved in the Given Pathways
calculate_pw_scores

Calculate Pathway Scores for Each Subject
cluster_graph_vis

Graph Visualization of Pathway Clustering
filterActiveSnws

Parse Active Subnetwork Search Output File and Filter the Subnetworks
example_active_snws

Example Active Subnetworks
go_bp_pathways

Gene Ontology - Biological Process Ontology Descriptions
biocarta_genes

BioCarta Gene Sets
go_cc_genes

Gene Ontology - Cellular Component Ontology Gene Sets
cluster_pathways

Cluster Pathways
biocarta_pathways

BioCarta Pathway Descriptions
run_pathfindR

Wrapper Function for pathfindR Workflow
RA_clustered

Example Output for the pathfindR Clustering Workflow - Rheumatoid Arthritis
summarize_enrichment_results

Summarize Enrichment Results
RA_exp_mat

Example Input for pathfindR - pathway z-scores
create_kappa_matrix

Create Kappa Statistics Matrix
custom_result

Custom Gene Set Enrichment Results
go_mf_pathways

Gene Ontology - Molecular Function Ontology Descriptions
hierarchical_pw_clustering

Hierarchical Clustering of Pathways
enrichment

Perform Enrichment Analysis for a Single Gene Set
kegg_pathways

KEGG Pathway Descriptions
go_cc_pathways

Gene Ontology - Cellular Component Ontology Descriptions
RA_input

Example Input for the pathfindR Enrichment Workflow - Rheumatoid Arthritis
pathfindR

pathfindR: A package for Pathway Enrichment Analysis Utilizing Active Subnetworks
RA_output

Example Output for the pathfindR Enrichment Workflow - Rheumatoid Arthritis
go_mf_genes

Gene Ontology - Molecular Function Ontology Gene Sets
plot_scores

Plot the Heatmap of Pathway Scores
reactome_genes

Reactome Gene Sets
fuzzy_pw_clustering

Heuristic Fuzzy Multiple-linkage Partitioning of Pathways
go_all_genes

Gene Ontology - All Ontology Gene Sets
hyperg_test

Hypergeometic Distribution-based Hypothesis Testing
input_processing

Process Input
return_pin_path

Return The Path to Given Protein-Protein Interaction Network (PIN)
reactome_pathways

Reactome Pathway Descriptions
visualize_pws

Create Pathway Diagrams