planttfhunter

The goal of planttfhunter is to identify plant transcription factors from protein sequence data and classify them into families and subfamilies using the classification schemes implemented in PlantTFDB and TAPscan, and into structure-based families, classes, and superclasses as in Plant-TFClass.

Installation instructions

Get the latest stable R release from CRAN. Then install planttfhunter from Bioconductor using the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("planttfhunter")

Or the development version from GitHub with:

BiocManager::install("almeidasilvaf/planttfhunter")

Citation

Below is the citation output from using citation('planttfhunter') in R. Please run this yourself to check for any updates on how to cite planttfhunter.

print(citation('planttfhunter'), bibtex = TRUE)
#> 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
#>   <https://doi.org/10.18129/B9.bioc.planttfhunter>, R package version
#>   1.13.0, <https://bioconductor.org/packages/planttfhunter>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @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 1.13.0},
#>     doi = {10.18129/B9.bioc.planttfhunter},
#>     url = {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
#> <https://doi.org/10.1093/nar/gkw982>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @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},
#>   }
#> 
#> 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
#> <https://doi.org/10.1111/tpj.17184>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @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},
#>   }
#> 
#> 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
#> <https://doi.org/10.1016/j.tplants.2023.06.023>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @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},
#>   }
#> 
#> 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).'

Please note that the planttfhunter project was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

Code of Conduct

Please note that the planttfhunter project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.