To cite planttfhunter in publications, please cite the package and the classification scheme(s) you used:

Almeida-Silva F, Van de Peer Y (2022). planttfhunter: Identification and classification of plant transcription factors. doi:10.18129/B9.bioc.planttfhunter. R package version 1.13.1, https://bioconductor.org/packages/planttfhunter.

Jin J, Tian F, Yang D, Meng Y, Kong L, Luo J, Gao G (2017). “PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants.” Nucleic Acids Research, 45(D1), D1040–D1045. doi:10.1093/nar/gkw982.

Petroll R, Varshney D, Hiltemann S, Finke H, Schreiber M, de Vries J, Rensing SA (2025). “Enhanced sensitivity of TAPscan v4 enables comprehensive analysis of streptophyte transcription factor evolution.” The Plant Journal, 121(1), e17184. doi:10.1111/tpj.17184.

Blanc-Mathieu R, Dumas R, Turchi L, Lucas J, Parcy F (2024). “Plant-TFClass: a structural classification for plant transcription factors.” Trends in Plant Science, 29(1), 40–51. doi:10.1016/j.tplants.2023.06.023.

Example of how to cite planttfhunter and the classification schemes (remove the schemes you did not use): 'TFs and their families were identified and classified with the R/Bioconductor package planttfhunter (Almeida-Silva and Van de Peer, 2022), using the classification schemes of PlantTFDB (Jin et al., 2017), TAPscan (Petroll et al., 2025), and Plant-TFClass (Blanc-Mathieu et al., 2024).'

Corresponding BibTeX entries:

  @Manual{planttfhunter,
    title = {planttfhunter: Identification and classification of plant
      transcription factors},
    author = {Fabrício Almeida-Silva and Yves {Van de Peer}},
    year = {2022},
    note = {R package version 1.13.1},
    doi = {10.18129/B9.bioc.planttfhunter},
    url = {https://bioconductor.org/packages/planttfhunter},
  }

  @Article{jin2017planttfdb,
    title = {PlantTFDB 4.0: toward a central hub for transcription
      factors and regulatory interactions in plants},
    author = {Jinpu Jin and Feng Tian and De-Chang Yang and Yu-Qi Meng
      and Lei Kong and Jingchu Luo and Ge Gao},
    journal = {Nucleic Acids Research},
    volume = {45},
    number = {D1},
    pages = {D1040--D1045},
    year = {2017},
    doi = {10.1093/nar/gkw982},
  }

  @Article{petroll2025tapscan,
    title = {Enhanced sensitivity of TAPscan v4 enables comprehensive
      analysis of streptophyte transcription factor evolution},
    author = {Romy Petroll and Deepti Varshney and Saskia Hiltemann and
      Hermann Finke and Mona Schreiber and Jan {de Vries} and Stefan A.
      Rensing},
    journal = {The Plant Journal},
    volume = {121},
    number = {1},
    pages = {e17184},
    year = {2025},
    doi = {10.1111/tpj.17184},
  }

  @Article{blancmathieu2024planttfclass,
    title = {Plant-TFClass: a structural classification for plant
      transcription factors},
    author = {Romain Blanc-Mathieu and Renaud Dumas and Laura Turchi
      and Jérémy Lucas and François Parcy},
    journal = {Trends in Plant Science},
    volume = {29},
    number = {1},
    pages = {40--51},
    year = {2024},
    doi = {10.1016/j.tplants.2023.06.023},
  }