README.md

In leekgroup/derfinderHelper: derfinder helper package

derfinderHelper

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.

leekgroup/derfinderHelper documentation built on May 10, 2023, 11:30 p.m.