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# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "pathfindR" in publications use:'
type: software
license: MIT
title: 'pathfindR: Enrichment Analysis Utilizing Active Subnetworks'
version: 3.0.2
doi: 10.3389/fgene.2019.00858
identifiers:
- type: doi
  value: 10.32614/CRAN.package.pathfindR
abstract: '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. <https://doi.org/10.3389/fgene.2019.00858>.'
authors:
- family-names: Ulgen
  given-names: Ege
  email: egeulgen@gmail.com
  orcid: https://orcid.org/0000-0003-2090-3621
- family-names: Ozisik
  given-names: Ozan
  email: ozanytu@gmail.com
  orcid: https://orcid.org/0000-0001-5980-8002
preferred-citation:
  type: article
  title: 'pathfindR: An R Package for Comprehensive Identification of Enriched Pathways
    in Omics Data Through Active Subnetworks'
  authors:
  - family-names: Ulgen
    given-names: Ege
    email: egeulgen@gmail.com
    orcid: https://orcid.org/0000-0003-2090-3621
  - family-names: Ozisik
    given-names: Ozan
    email: ozanytu@gmail.com
    orcid: https://orcid.org/0000-0001-5980-8002
  - family-names: Sezerman
    given-names: Osman Ugur
  journal: Frontiers in Genetics
  volume: '10'
  year: '2019'
  url: https://doi.org/10.3389/fgene.2019.00858
  start: '858'
  doi: 10.3389/fgene.2019.00858
repository: https://cran.r-universe.dev
repository-code: https://github.com/egeulgen/pathfindR
commit: cbbd36331254991e8eba8ad4dab89702ff704d67
url: https://egeulgen.github.io/pathfindR/
date-released: '2026-07-01'
contact:
- family-names: Ulgen
  given-names: Ege
  email: egeulgen@gmail.com
  orcid: https://orcid.org/0000-0003-2090-3621