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

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

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 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.

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 r BiocStyle::Githubpkg('lcolladotor/biocthis') package.