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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 "dorothea" in publications use:'
type: software
license: GPL-3.0-only
title: 'dorothea: Collection Of Human And Mouse TF Regulons'
version: 1.25.0
doi: 10.1101/gr.240663.118
identifiers:
- type: doi
  value: 10.32614/CRAN.package.dorothea
abstract: DoRothEA is a gene regulatory network containing signed transcription factor
  (TF) - target gene interactions. DoRothEA regulons, the collection of a TF and its
  transcriptional targets, were curated and collected from different types of evidence
  for both human and mouse. A confidence level was assigned to each TF-target interaction
  based on the number of supporting evidence.
authors:
- family-names: Badia-i-Mompel
  given-names: Pau
  email: pau.badia@uni-heidelberg.de
  orcid: https://orcid.org/0000-0002-1004-3923
- family-names: Dimitrov
  given-names: Daniel
  email: daniel.dimitrov@uni-heidelberg.de
  orcid: https://orcid.org/0000-0002-5197-2112
- family-names: Holland
  given-names: Christian H.
  email: cholland2408@gmail.com
  orcid: https://orcid.org/0000-0002-3060-5786
- family-names: Garcia-Alonso
  given-names: Luz
preferred-citation:
  type: article
  title: Benchmark and integration of resources for the estimation of human transcription
    factor activities
  authors:
  - family-names: Garcia-Alonso
    given-names: Luz
  - family-names: Holland
    given-names: Christian H.
    email: cholland2408@gmail.com
    orcid: https://orcid.org/0000-0002-3060-5786
  - family-names: Ibrahim
    given-names: Mahmoud M.
  - family-names: Turei
    given-names: Denes
  - family-names: Saez-Rodriguez
    given-names: Julio
  journal: Genome Research
  year: '2019'
  doi: 10.1101/gr.240663.118
repository: https://bioc.r-universe.dev
repository-code: https://github.com/saezlab/dorothea
commit: 4feba311dcfeaea16ba2302675d7227a322b214b
url: https://saezlab.github.io/dorothea/
date-released: '2026-04-28'
contact:
- family-names: Badia-i-Mompel
  given-names: Pau
  email: pau.badia@uni-heidelberg.de
  orcid: https://orcid.org/0000-0002-1004-3923
references:
- type: article
  title: 'decoupleR: ensemble of computational methods to infer biological activities
    from omics data'
  authors:
  - family-names: Badia-i-Mompel
    given-names: Pau
  - family-names: Santiago
    given-names: Jesús Vélez
  - family-names: Braunger
    given-names: Jana
  - family-names: Geiss
    given-names: Celina
  - family-names: Dimitrov
    given-names: Daniel
  - family-names: Müller-Dott
    given-names: Sophia
  - family-names: Taus
    given-names: Petr
  - family-names: Dugourd
    given-names: Aurelien
  - family-names: Holland
    given-names: Christian H.
  - family-names: Flores
    given-names: Ricardo O. Ramirez
  - family-names: Saez-Rodriguez
    given-names: Julio
  journal: Bioinformatics Advances
  year: '2022'
  doi: 10.1093/bioadv/vbac016
- type: article
  title: Expanding the coverage of regulons from high-confidence prior knowledge for
    accurate estimation of transcription factor activities
  authors:
  - family-names: Müller-Dott
    given-names: Sophia
  - family-names: Tsirvouli
    given-names: Eirini
  - family-names: Vázquez
    given-names: Miguel
  - family-names: Flores
    given-names: Ricardo O. Ramirez
  - family-names: Badia-i-Mompel
    given-names: Pau
  - family-names: Fallegger
    given-names: Robin
  - family-names: Lægreid
    given-names: Astrid
  - family-names: Saez-Rodriguez
    given-names: Julio
  journal: bioRxiv
  year: '2023'
  doi: 10.1101/2023.03.30.534849