<!-- README.md is generated from README.Rmd. Please edit that file --> # planttfhunter <img src="man/figures/logo.png" align="right" height="139" /> <!-- badges: start --> [](https://github.com/almeidasilvaf/planttfhunter/issues) [](https://lifecycle.r-lib.org/articles/stages.html#stable) [](https://github.com/almeidasilvaf/planttfhunter/actions) [](https://codecov.io/gh/almeidasilvaf/planttfhunter?branch=devel) <!-- badges: end --> 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](https://doi.org/10.1093/nar/gkz1020). ## Installation instructions Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install **planttfhunter** from [Bioconductor](http://bioconductor.org/) using the following code: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("planttfhunter") ``` And the development version from [GitHub](https://github.com/almeidasilvaf/planttfhunter) with: ``` r 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**. ``` r 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](http://bioconductor.org/about/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](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/) through *[usethis](https://CRAN.R-project.org/package=usethis)*, *[remotes](https://CRAN.R-project.org/package=remotes)*, and *[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)* customized to use [Bioconductor’s docker containers](https://www.bioconductor.org/help/docker/) and *[BiocCheck](https://bioconductor.org/packages/3.15/BiocCheck)*. - Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and *[covr](https://CRAN.R-project.org/package=covr)*. - The [documentation website](http://almeidasilvaf.github.io/planttfhunter) is automatically updated thanks to *[pkgdown](https://CRAN.R-project.org/package=pkgdown)*. - The documentation is formatted thanks to *[devtools](https://CRAN.R-project.org/package=devtools)* and *[roxygen2](https://CRAN.R-project.org/package=roxygen2)*. This package was developed using *[biocthis](https://bioconductor.org/packages/3.15/biocthis)*.