Build and access GenomicState objects for use with derfinder tools from sources like Gencode (original) (raw)

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().

Installation instructions

Get the latest stable R release from CRAN. Then install GenomicState from Bioconductor using the following code:

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.