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.
Get the latest stable R release from
CRAN. Then install dasper from
Bioconductor using 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")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 (2021). _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 1.3.8, <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 = {2021},
#> url = {http://www.bioconductor.org/packages/dasper},
#> note = {https://github.com/dzhang32/dasper - R package version 1.3.8},
#> 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.
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.
- 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.
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