<!-- README.md is generated from README.Rmd. Please edit that file -->
# derfinderHelper
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Helper package for
[derfinder](http://www.bioconductor.org/packages/derfinder).
## Documentation
For more information about `derfinderHelper` check the vignettes
[through Bioconductor](http://bioconductor.org/packages/derfinderHelper)
or at the [documentation
website](http://leekgroup.github.io/derfinderHelper).
## Installation instructions
Get the latest stable `R` release from
[CRAN](http://cran.r-project.org/). Then install `derfinderHelper` from
[Bioconductor](http://bioconductor.org/) using the following code:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("derfinderHelper")
```
## Citation
Below is the citation output from using `citation('derfinderHelper')` in
R. Please run this yourself to check for any updates on how to cite
**derfinderHelper**.
``` r
print(citation("derfinderHelper"), bibtex = TRUE)
#>
#> Collado-Torres L, Jaffe AE, Leek JT (2017). _derfinderHelper: derfinder
#> helper package_. doi: 10.18129/B9.bioc.derfinderHelper (URL:
#> https://doi.org/10.18129/B9.bioc.derfinderHelper),
#> https://github.com/leekgroup/derfinderHelper - R package version
#> 1.25.1, <URL: http://www.bioconductor.org/packages/derfinderHelper>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {derfinderHelper: derfinder helper package},
#> author = {Leonardo Collado-Torres and Andrew E. Jaffe and Jeffrey T. Leek},
#> year = {2017},
#> url = {http://www.bioconductor.org/packages/derfinderHelper},
#> note = {https://github.com/leekgroup/derfinderHelper - R package version 1.25.1},
#> doi = {10.18129/B9.bioc.derfinderHelper},
#> }
#>
#> Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B,
#> Irizarry RA, Leek JT, Jaffe AE (2017). "Flexible expressed region
#> analysis for RNA-seq with derfinder." _Nucl. Acids Res._. doi:
#> 10.1093/nar/gkw852 (URL: https://doi.org/10.1093/nar/gkw852), <URL:
#> http://nar.oxfordjournals.org/content/early/2016/09/29/nar.gkw852>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {Flexible expressed region analysis for RNA-seq with derfinder},
#> author = {Leonardo Collado-Torres and Abhinav Nellore and Alyssa C. Frazee and Christopher Wilks and Michael I. Love and Ben Langmead and Rafael A. Irizarry and Jeffrey T. Leek and Andrew E. Jaffe},
#> year = {2017},
#> journal = {Nucl. Acids Res.},
#> doi = {10.1093/nar/gkw852},
#> url = {http://nar.oxfordjournals.org/content/early/2016/09/29/nar.gkw852},
#> }
```
Please note that the `derfinderHelper` 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 derfinderHelper project is released with a
[Contributor Code of
Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
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)*,
*[sysreqs](https://github.com/r-hub/sysreqs)* 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/3.12/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://leekgroup.github.io/derfinderHelper) is
automatically updated thanks to
*[pkgdown](https://CRAN.R-project.org/package=pkgdown)*.
- The code is styled automatically thanks to
*[styler](https://CRAN.R-project.org/package=styler)*.
- The documentation is formatted thanks to
*[devtools](https://CRAN.R-project.org/package=devtools)* and
*[roxygen2](https://CRAN.R-project.org/package=roxygen2)*.
For more details, check the `dev` directory.
