The goal of ExampleBiocWorkshop2023
is to demo how to make an
R/Bioconductor workshop package.
Get the latest stable R
release from
CRAN. Then install
ExampleBiocWorkshop2023
from Bioconductor
using the following code:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("ExampleBiocWorkshop2023")
And the development version from GitHub with:
BiocManager::install("lcolladotor/ExampleBiocWorkshop2023")
This is a basic example which shows you how to solve a common problem:
library("ExampleBiocWorkshop2023")
## basic example code
What is special about using README.Rmd
instead of just README.md
?
You can include R chunks like so:
summary(cars)
#> speed dist
#> Min. : 4.0 Min. : 2.00
#> 1st Qu.:12.0 1st Qu.: 26.00
#> Median :15.0 Median : 36.00
#> Mean :15.4 Mean : 42.98
#> 3rd Qu.:19.0 3rd Qu.: 56.00
#> Max. :25.0 Max. :120.00
You’ll still need to render README.Rmd
regularly, to keep README.md
up-to-date.
You can also embed plots, for example:
In that case, don’t forget to commit and push the resulting figure files, so they display on GitHub!
Below is the citation output from using
citation('ExampleBiocWorkshop2023')
in R. Please run this yourself to
check for any updates on how to cite ExampleBiocWorkshop2023.
print(citation('ExampleBiocWorkshop2023'), bibtex = TRUE)
#>
#> To cite package 'ExampleBiocWorkshop2023' in publications use:
#>
#> lcolladotor (2023). _Demo Bioconductor package 2023_.
#> doi:10.18129/B9.bioc.ExampleBiocWorkshop2023
#> <https://doi.org/10.18129/B9.bioc.ExampleBiocWorkshop2023>,
#> https://github.com/lcolladotor/ExampleBiocWorkshop2023/ExampleBiocWorkshop2023
#> - R package version 0.99.0,
#> <http://www.bioconductor.org/packages/ExampleBiocWorkshop2023>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {Demo Bioconductor package 2023},
#> author = {{lcolladotor}},
#> year = {2023},
#> url = {http://www.bioconductor.org/packages/ExampleBiocWorkshop2023},
#> note = {https://github.com/lcolladotor/ExampleBiocWorkshop2023/ExampleBiocWorkshop2023 - R package version 0.99.0},
#> doi = {10.18129/B9.bioc.ExampleBiocWorkshop2023},
#> }
#>
#> lcolladotor (2023). "Demo Bioconductor package 2023." _bioRxiv_.
#> doi:10.1101/TODO <https://doi.org/10.1101/TODO>,
#> <https://www.biorxiv.org/content/10.1101/TODO>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {Demo Bioconductor package 2023},
#> author = {{lcolladotor}},
#> year = {2023},
#> journal = {bioRxiv},
#> doi = {10.1101/TODO},
#> url = {https://www.biorxiv.org/content/10.1101/TODO},
#> }
Please note that the ExampleBiocWorkshop2023
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.
Please note that the ExampleBiocWorkshop2023
project is released with
a Contributor Code of
Conduct. By
contributing to this project, you agree to abide by its terms.
- 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.