The goal of BiocPkgToolsPlus is to demonstrate use of BiocPkgTools functionality to study the composition the Bioconductor package ecosystem. This is meant to learn about packages, identify trends and issues in package annotations, and inform policies for package development and maintenance.
Installation instructions
Get the latest stable R release from CRAN. Then install BiocPkgToolsPlus from Bioconductor using the following code:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("BiocPkgToolsPlus")And the development version from GitHub with:
BiocManager::install("kevinrue/BiocPkgToolsPlus")Example
This is a basic example which shows you how to get the names of packages annotated with a given set of biocViews.
library("BiocPkgToolsPlus")
#> Loading required package: biocViews
get_packages_by_views(c("Spatial", "Transcriptomics", "SingleCell"))
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#> BioCsoft: https://bioconductor.org/packages/3.21/bioc
#> BioCann: https://bioconductor.org/packages/3.21/data/annotation
#> BioCexp: https://bioconductor.org/packages/3.21/data/experiment
#> BioCworkflows: https://bioconductor.org/packages/3.21/workflows
#> BioCbooks: https://bioconductor.org/packages/3.21/books
#> CRAN: https://packagemanager.posit.co/cran/latest
#> [1] "CARDspa" "clustSIGNAL" "concordexR"
#> [4] "DESpace" "escheR" "ggsc"
#> [7] "ggspavis" "hoodscanR" "nnSVG"
#> [10] "OSTA.data" "retrofit" "SEraster"
#> [13] "smoothclust" "smoppix" "SpaceTrooper"
#> [16] "spacexr" "SpatialExperiment" "SpatialExperimentIO"
#> [19] "spoon" "SpotClean" "stPipe"
#> [22] "SVP" "tidySpatialExperiment" "CatsCradle"
#> [25] "scFeatures" "SpaceMarkers"Citation
Below is the citation output from using citation('BiocPkgToolsPlus') in R. Please run this yourself to check for any updates on how to cite BiocPkgToolsPlus.
print(citation('BiocPkgToolsPlus'), bibtex = TRUE)
#> To cite package 'BiocPkgToolsPlus' in publications use:
#>
#> kevinrue (2025). _Demonstration of a Bioconductor Package_.
#> doi:10.18129/B9.bioc.BiocPkgToolsPlus
#> <https://doi.org/10.18129/B9.bioc.BiocPkgToolsPlus>,
#> https://github.com/kevinrue/BiocPkgToolsPlus/BiocPkgToolsPlus - R
#> package version 0.99.0,
#> <http://www.bioconductor.org/packages/BiocPkgToolsPlus>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {Demonstration of a Bioconductor Package},
#> author = {{kevinrue}},
#> year = {2025},
#> url = {http://www.bioconductor.org/packages/BiocPkgToolsPlus},
#> note = {https://github.com/kevinrue/BiocPkgToolsPlus/BiocPkgToolsPlus - R package version 0.99.0},
#> doi = {10.18129/B9.bioc.BiocPkgToolsPlus},
#> }
#>
#> kevinrue (2025). "Demonstration of a Bioconductor Package."
#> _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 = {Demonstration of a Bioconductor Package},
#> author = {{kevinrue}},
#> year = {2025},
#> journal = {bioRxiv},
#> doi = {10.1101/TODO},
#> url = {https://www.biorxiv.org/content/10.1101/TODO},
#> }Please note that the BiocPkgToolsPlus 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 BiocPkgToolsPlus 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.
Code of Conduct
Please note that the BiocPkgToolsPlus project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.