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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# 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 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("planttfhunter")
```
And the development version from
[GitHub](https://github.com/almeidasilvaf/planttfhunter) with:
```{r 'install_dev', eval = FALSE}
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 'citation', eval = requireNamespace('planttfhunter')}
print(citation('planttfhunter'), bibtex = TRUE)
```
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 `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.
* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.
* The [documentation website](http://almeidasilvaf.github.io/planttfhunter) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.
* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.
This package was developed using `r BiocStyle::Biocpkg('biocthis')`.