ODER

The goal of ODER is to Optimise the Definition of Expressed Regions. ODER is a packaged form of the method developed in the Zhang et al. 2020 publication: Incomplete annotation has a disproportionate impact on our understanding of Mendelian and complex neurogenetic disorders. For a more detailed explanation of using ODER, please see the vignette. For more explanation of the methodology behind ODER, see the mehtods section of the original publication.

Installation instructions

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

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("ODER")

And the development version from GitHub with:

BiocManager::install("eolagbaju/ODER")

Citation

Below is the citation output from using citation('ODER') in R. Please run this yourself to check for any updates on how to cite ODER.

message(citation("ODER"), bibtex = TRUE)
#> list(title = "Optimising the Definition of Expressed Regions", author = list(list(given = NULL, family = "eolagbaju", role = NULL, email = NULL, comment = NULL)), year = "2021", url = "http://www.bioconductor.org/packages/ODER", note = "https://github.com/eolagbaju/ODER/ODER - R package version 0.99.31", doi = "10.18129/B9.bioc.ODER")list(title = "Optimising the Definition of Expressed Regions", author = list(list(given = NULL, family = "eolagbaju", role = NULL, email = NULL, comment = NULL)), year = "2021", journal = "bioRxiv", doi = "10.1101/TODO", url = "https://www.biorxiv.org/content/10.1101/TODO")TRUE

Please note that the ODER 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 ODER 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, 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.