GitHub - LieberInstitute/GenomicState: Build and access GenomicState objects for use with derfinder tools from sources like Gencode (original) (raw)

GenomicState

This package provides functions for building GenomicState objects from diverse annotation sources such asGencode. It also provides a way to load pre-computed GenomicState objects if you are working at JHPCE. These GenomicState objects are normally created usingderfinder::makeGenomicState()and can be used for annotating regions withderfinder::annotateRegions()which are in turn used byderfinderPlot::plotRegionCoverage().

Documentation

For more information about GenomicState check the vignettes through Bioconductor or at thedocumentation website.

Installation instructions

Get the latest stable R release fromCRAN. Then install GenomicState fromBioconductor 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 citeGenomicState.

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 aContributor 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 actionsthrough usethis,remotes,sysreqs and_rcmdcheck_ customized to use Bioconductor’s docker containers and_BiocCheck_.
• Code coverage assessment is possible thanks tocodecov 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_.