To cite package ‘dorothea’ in publications use:

  Garcia-Alonso L, Holland CH, Ibrahim MM, Turei D, Saez-Rodriguez J.
  'Benchmark and integration of resources for the estimation of human
  transcription factor activities.' Genome Research. 2019. DOI:
  10.1101/gr.240663.118.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Luz Garcia-Alonso and Christian H. Holland and Mahmoud M. Ibrahim and Denes Turei and Julio Saez-Rodriguez},
    title = {Benchmark and integration of resources for the estimation of human transcription factor activities},
    journal = {Genome Research},
    year = {2019},
    doi = {10.1101/gr.240663.118},
  }

  Badia-i-Mompel P., Vélez Santiago J., Braunger J., Geiss C., Dimitrov
  D., Müller-Dott S., Taus P., Dugourd A., Holland C.H., Ramirez Flores
  R.O.  and Saez-Rodriguez J. 2022. decoupleR: Ensemble of
  computational methods to infer biological activities from omics data.
  Bioinformatics Advances.  https://doi.org/10.1093/bioadv/vbac016

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Pau Badia-i-Mompel and Jesús Vélez Santiago and Jana Braunger and Celina Geiss and Daniel Dimitrov and Sophia Müller-Dott and Petr Taus and Aurelien Dugourd and Christian H. Holland and Ricardo O. Ramirez Flores and Julio Saez-Rodriguez},
    title = {decoupleR: ensemble of computational methods to infer biological activities from omics data},
    journal = {Bioinformatics Advances},
    year = {2022},
    doi = {https://doi.org/10.1093/bioadv/vbac016},
  }

  Müller-Dott S., Tsirvouli E., Vázquez M., Ramirez Flores R.O.,
  Badia-i-Mompel P., Fallegger R., Lægreid A. and Saez-Rodriguez J.
  2023.  Expanding the coverage of regulons from high-confidence prior
  knowledge for accurate estimation of transcription factor activities.
  bioRxiv.  https://doi.org/10.1101/2023.03.30.534849

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Sophia Müller-Dott and Eirini Tsirvouli and Miguel Vázquez and Ricardo O. Ramirez Flores and Pau Badia-i-Mompel and Robin Fallegger and Astrid Lægreid and Julio Saez-Rodriguez},
    title = {Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities},
    journal = {bioRxiv},
    year = {2023},
    doi = {https://doi.org/10.1101/2023.03.30.534849},
  }
