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 scheme implemented in PlantTFDB.

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")

And 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 package 'planttfhunter' in publications use:
#> 
#>   Almeida-Silva F, Van de Peer Y (2022). _planttfhunter: Identification
#>   and classification of plant transcription factors_. R package version
#>   0.99.0, <https://github.com/almeidasilvaf/planttfhunter>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {planttfhunter: Identification and classification of plant transcription factors},
#>     author = {Fabrício Almeida-Silva and Yves {Van de Peer}},
#>     year = {2022},
#>     note = {R package version 0.99.0},
#>     url = {https://github.com/almeidasilvaf/planttfhunter},
#>   }

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.

Development tools

Continuous code testing is possible thanks to GitHub actions through usethis, remotes, and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
Code coverage assessment is possible thanks to codecov and covr.
The documentation website is automatically updated thanks to pkgdown.
The documentation is formatted thanks to devtools and roxygen2.

This package was developed using biocthis.