rutils

The goal of rutils is to house some of my commonly used functions.

Installation instructions

There is no plan to ever submit this code to CRAN or Bioconductor. This code was developed for personal use. If you would like to install the development version from GitHub you can use the following command:

remotes::install_github("RHReynolds/rutils")

Note: If you are running R (< 4.0), installation may return the error that GOSemSim (v2.16.1) and/or rrvgo are not available for your R version. However, these packages do not actually have a dependency on R (>= 4.0) -- the error occurs because these packages cannot be found using your version of BioConductor (which is likely to be < 3.12). A workaround to this issue is to install the development versions of these packages directly from GitHub, using the following command:

# If GOSemSim successfully installed, simply remove from command
remotes::install_github(c("GuangchuangYu/GOSemSim", "ssayols/rrvgo"))

The downside of this is, of course, that these are development versions, and thus may not be entirely stable, so be sure to check in on these packages every so often to see if there have been any major bug fixes.

Citation

Below is the citation output from using citation('rutils') in R. Please run this yourself to check for any updates on how to cite rutils.

print(citation("rutils"), bibtex = TRUE)
#> 
#> RHReynolds (2022). _Common utility functions_. doi:
#> 10.5281/zenodo.6127446 (URL: https://doi.org/10.5281/zenodo.6127446),
#> https://github.com/RHReynolds/rutils - R package version 0.99.2, <URL:
#> https://github.com/RHReynolds/rutils>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {Common utility functions},
#>     author = {{RHReynolds}},
#>     year = {2022},
#>     url = {https://github.com/RHReynolds/rutils},
#>     note = {https://github.com/RHReynolds/rutils - R package version 0.99.2},
#>     doi = {10.5281/zenodo.6127446},
#>   }

Please note that the rutils 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 rutils 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, 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.

This package was developed using biocthis.