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pathfindR (version 1.2.3)

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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Version

Install

install.packages('pathfindR')

Monthly Downloads

1,346

Version

1.2.3

License

MIT + file LICENSE

Issues

0

Pull Requests

1

Stars

190

Forks

27

Maintainer

Ege Ulgen

Last Published

October 26th, 2018

Functions in pathfindR (1.2.3)

RA_input

Example Input for the pathfindR Enrichment Workflow - Rheumatoid Arthritis
RA_output

Example Output for the pathfindR Enrichment Workflow - Rheumatoid Arthritis
RA_clustered

Example Output for the pathfindR Clustering Workflow - Rheumatoid Arthritis
RA_exp_mat

Example Input for pathfindR - pathway z-scores
go_bp_genes

Gene Ontology - Biological Process Ontology Gene Sets
go_mf_genes

Gene Ontology - Molecular Function Ontology Gene Sets
go_mf_pathways

Gene Ontology - Molecular Function Ontology Descriptions
go_bp_pathways

Gene Ontology - Biological Process Ontology Descriptions
parseActiveSnwSearch

Parse Active Subnetwork Search Output File
pathfindR

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

Annotate Involved Genes In Pathways and Visualize Pathways
calculate_pw_scores

Calculate Pathway Scores for Each Subject
biocarta_genes

BioCarta Gene Sets
biocarta_pathways

BioCarta Pathway Descriptions
plot_scores

Plot the Heatmap of Pathway Scores
go_cc_genes

Gene Ontology - Cellular Component Ontology Gene Sets
calculate_pwd

Calculate Pairwise Distances Between Given Pathways
go_cc_pathways

Gene Ontology - Cellular Component Ontology Descriptions
kegg_genes

KEGG Gene Sets
kegg_pathways

KEGG Pathway Descriptions
input_processing

Process Input
input_testing

Input Testing
return_pin_path

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

Wrapper Function for pathfindR Workflow
enrichment

Perform Enrichment Analysis
enrichment_chart

Plot the Bubble Chart of Enrichment Results
reactome_genes

Reactome Gene Sets
reactome_pathways

Reactome Pathway Descriptions
choose_clusters

Cluster Pathways and Partition the Dendrogram
custom_result

Custom Gene Set Enrichment Results