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# CITATION 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 "OmnipathR" in publications use:'
type: software
license: MIT
title: 'OmnipathR: OmniPath web service client and more'
version: 3.13.1
doi: 10.15252/msb.20209923
abstract: A client for the OmniPath web service (https://www.omnipathdb.org) and many
  other resources. It also includes functions to transform and pretty print some of
  the downloaded data, functions to access a number of other resources such as BioPlex,
  ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome,
  HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons,
  Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al.
  2011. Furthermore, OmnipathR features a close integration with the NicheNet method
  for ligand activity prediction from transcriptomics data, and its R implementation
  `nichenetr` (available only on github).
authors:
- family-names: Valdeolivas
  given-names: Alberto
  email: alvaldeolivas@gmail.com
  orcid: https://orcid.org/0000-0001-5482-9023
- family-names: Turei
  given-names: Denes
  email: turei.denes@gmail.com
  orcid: https://orcid.org/0000-0002-7249-9379
- family-names: Gabor
  given-names: Attila
  orcid: https://orcid.org/0000-0002-0776-1182
preferred-citation:
  type: article
  title: Integrated intra- and intercellular signaling knowledge for multicellular
    omics analysis
  authors:
  - family-names: Turei
    given-names: Denes
    email: turei.denes@gmail.com
    orcid: https://orcid.org/0000-0002-7249-9379
  - family-names: Valdeolivas
    given-names: Alberto
    email: alvaldeolivas@gmail.com
    orcid: https://orcid.org/0000-0001-5482-9023
  - family-names: Gul
    given-names: Lejla
  - family-names: Palacio-Escat
    given-names: Nicolas
  - family-names: Klein
    given-names: Michal
  - family-names: Ivanova
    given-names: Olga
  - family-names: Olbei
    given-names: Marton
  - family-names: Gabor
    given-names: Attila
    orcid: https://orcid.org/0000-0002-0776-1182
  - family-names: Theis
    given-names: Fabian
  - family-names: Modos
    given-names: Dezso
  - family-names: Korcsmaros
    given-names: Tamas
  - family-names: Saez-Rodriguez
    given-names: Julio
  journal: Molecular Systems Biology
  year: '2021'
  doi: 10.15252/msb.20209923
repository: https://bioc.r-universe.dev
repository-code: https://github.com/saezlab/OmnipathR
url: https://r.omnipathdb.org/
contact:
- family-names: Turei
  given-names: Denes
  email: turei.denes@gmail.com
  orcid: https://orcid.org/0000-0002-7249-9379
references:
- type: article
  title: 'OmniPath: guidelines and gateway for literature-curated signaling pathway
    resources'
  authors:
  - family-names: Turei
    given-names: Denes
  - family-names: Korcsmaros
    given-names: Tamas
  - family-names: Saez-Rodriguez
    given-names: Julio
  journal: Nature Methods
  year: '2016'
- type: generic
  title: 'OmnipathR: client for the OmniPath web service'
  authors:
  - family-names: Valdeolivas
    given-names: Alberto
  - family-names: Turei
    given-names: Denes
  - family-names: Gabor
    given-names: Attila
  notes: Bioconductor Package
  year: '2019'