GenomicState

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.