README.md

In LieberInstitute/GenomicState: Build and access GenomicState objects for use with derfinder tools from sources like Gencode

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.

LieberInstitute/GenomicState documentation built on May 12, 2023, 5:15 p.m.