Helper package for derfinder.
Documentation
For more information about derfinderHelper check the vignettes through Bioconductor or at the documentation website.
Installation instructions
Get the latest stable R release from CRAN. Then install derfinderHelper from Bioconductor using the following code:
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.
print(citation("derfinderHelper"), bibtex = TRUE)
#> To cite package 'derfinderHelper' in publications use:
#>
#> Collado-Torres L, Jaffe AE, Leek JT (2017). _derfinderHelper:
#> derfinder helper package_. doi:10.18129/B9.bioc.derfinderHelper
#> <https://doi.org/10.18129/B9.bioc.derfinderHelper>,
#> https://github.com/leekgroup/derfinderHelper - R package version
#> 1.35.0, <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 1.35.0},
#> 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 <https://doi.org/10.1093/nar/gkw852>,
#> <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. 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, sysreqs 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 code is styled automatically thanks to styler.
- The documentation is formatted thanks to devtools and roxygen2.
For more details, check the dev directory.
