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

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/"
)

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)

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 r BiocStyle::CRANpkg('usethis'), r BiocStyle::CRANpkg('remotes'), r BiocStyle::Githubpkg('r-hub/sysreqs') and r BiocStyle::CRANpkg('rcmdcheck') customized to use Bioconductor's docker containers and r BiocStyle::Biocpkg('BiocCheck').
• Code coverage assessment is possible thanks to codecov and r BiocStyle::CRANpkg('covr').
• The documentation website is automatically updated thanks to r BiocStyle::CRANpkg('pkgdown').
• The code is styled automatically thanks to r BiocStyle::CRANpkg('styler').
• The documentation is formatted thanks to r BiocStyle::CRANpkg('devtools') and r BiocStyle::CRANpkg('roxygen2').

For more details, check the dev directory.

This package was developed using r BiocStyle::Biocpkg('biocthis').

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