README.md

In dasper: Detecting abberant splicing events from RNA-sequencing data

dasper

The aim of dasper is to detect aberrant splicing events from RNA-seq data. By comparing patient RNA-seq data to a set of controls, dasper will score each splicing event in the patient representing the degree to which that splicing event looks abnormal. For a detailed guide on the usage of dasper, check out the vignette here.

Installation instructions

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

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

BiocManager::install("dasper")

And the development version from GitHub with:

BiocManager::install("dzhang32/dasper")

Citation

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

print(citation("dasper"), bibtex = TRUE)
#> 
#> dzhang32 (2020). _Detecting abberant splicing events from
#> RNA-sequencing data_. doi: 10.18129/B9.bioc.dasper (URL:
#> https://doi.org/10.18129/B9.bioc.dasper),
#> https://github.com/dzhang32/dasper - R package version 0.99.16, <URL:
#> http://www.bioconductor.org/packages/dasper>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {Detecting abberant splicing events from RNA-sequencing data},
#>     author = {{dzhang32}},
#>     year = {2020},
#>     url = {http://www.bioconductor.org/packages/dasper},
#>     note = {https://github.com/dzhang32/dasper - R package version 0.99.16},
#>     doi = {10.18129/B9.bioc.dasper},
#>   }
#> 
#> dzhang32 (2020). "Detecting abberant splicing events from
#> RNA-sequencing data." _bioRxiv_. doi: 10.1101/TODO (URL:
#> https://doi.org/10.1101/TODO), <URL:
#> https://www.biorxiv.org/content/10.1101/TODO>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {Detecting abberant splicing events from RNA-sequencing data},
#>     author = {{dzhang32}},
#>     year = {2020},
#>     journal = {bioRxiv},
#>     doi = {10.1101/TODO},
#>     url = {https://www.biorxiv.org/content/10.1101/TODO},
#>   }

Please note that the dasper 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 dasper 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.

In particular, I am very grateful to Leo for his time and advice throughout the development of dasper. The transition of dasper Bioconductor-friendly package was made possible thanks to his biocthis package.

dasper documentation built on Nov. 8, 2020, 7:28 p.m.