This package provides functions for building GenomicState objects from diverse annotation sources such as Gencode. It also provides a way to load pre-computed GenomicState objects if you are working at JHPCE. These GenomicState objects are normally created using derfinder::makeGenomicState() and can be used for annotating regions with derfinder::annotateRegions() which are in turn used by derfinderPlot::plotRegionCoverage().
Documentation
For more information about GenomicState check the vignettes through Bioconductor or at the documentation website.
Installation instructions
Get the latest stable R release from CRAN. Then install GenomicState from Bioconductor using the following code:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("GenomicState")Citation
Below is the citation output from using citation('GenomicState') in R. Please run this yourself to check for any updates on how to cite GenomicState.
print(citation("GenomicState"), bibtex = TRUE)
#> To cite package 'GenomicState' in publications use:
#>
#> Collado-Torres L (2023). _Build and access GenomicState objects for
#> use with derfinder tools from sources like Gencode_.
#> doi:10.18129/B9.bioc.GenomicState
#> <https://doi.org/10.18129/B9.bioc.GenomicState>,
#> https://github.com/LieberInstitute/GenomicState - R package version
#> 0.99.15, <http://www.bioconductor.org/packages/GenomicState>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {Build and access GenomicState objects for use with derfinder tools from sources like Gencode},
#> author = {Leonardo Collado-Torres},
#> year = {2023},
#> url = {http://www.bioconductor.org/packages/GenomicState},
#> note = {https://github.com/LieberInstitute/GenomicState - R package version 0.99.15},
#> doi = {10.18129/B9.bioc.GenomicState},
#> }Please note that the GenomicState 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 derfinderPlot 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.
This package was developed using biocthis.
