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.

Depends: R (>= 3.4), knitr, shiny, pathview

org.Hs.eg.db, ggplot2, fpc, grDevices, igraph

Title: Enrichment Analysis Utilizing Active Subnetworks
Description: 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>.
Imports: DBI, AnnotationDbi, doParallel, foreach, rmarkdown,
org.Hs.eg.db, ggplot2, ggraph, fpc, grDevices, igraph, R.utils,

org.Hs.eg.db, ggplot2, ggraph, ggupset, fpc, grDevices, igraph,
R.utils, magick, msigdbr, KEGGREST, KEGGgraph, knitr
Author: Ege Ulgen [cre, cph] (<https://orcid.org/0000-0003-2090-3621>),

Description: This is a data-only package, containing data needed to run the CRAN
package 'pathfindR', a package for enrichment analysis utilizing active
subnetworks. This package contains protein-protein interaction network data,
data related to gene sets and example input/output data.