1 Basics

1.1 Install dasper

R is an open-source statistical environment which can be easily modified to enhance its functionality via packages. dasper is a R package available via the Bioconductor repository for packages. R can be installed on any operating system from CRAN after which you can install dasper by using the following commands in your R session:

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

BiocManager::install("dzhang32/dasper")

## Check that you have a valid Bioconductor installation
BiocManager::valid()

1.2 Required knowledge

The expected input of dasper are junctions reads (e.g. directly outputted from an aligner such as STAR or extracted from a BAM file (e.g. using megadepth) and coverage in the form of BigWig files (which can be generated from BAM files using megadepth or RSeQC). dasper is based on many other packages and in particular in those that have implemented the infrastructure needed for dealing with RNA-sequencing data. The packages SummarizedExperiment and GenomicRanges are used throughout, therefore familiarity with these packages will greatly help in interpreting the output of dasper.

If you are asking yourself the question “Where do I start using Bioconductor?” you might be interested in this blog post. Or if you find the structure of a SummarizedExperiment unclear, you might consider checking out this manual.

1.3 Asking for help

As package developers, we try to explain clearly how to use our packages and in which order to use the functions. But R and Bioconductor have a steep learning curve so it is critical to learn where to ask for help. The blog post quoted above mentions some but we would like to highlight the Bioconductor support site as the main resource for getting help: remember to use the dasper tag and check the older posts. Other alternatives are available such as creating GitHub issues and tweeting. However, please note that if you want to receive help you should adhere to the posting guidelines. It is particularly critical that you provide a small reproducible example and your session information so package developers can track down the source of the error.

1.4 Citing dasper

We hope that dasper will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!

## Citation info
citation("dasper")
#> 
#> 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 1.2.0, <URL:
#> http://www.bioconductor.org/packages/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>.
#> 
#> To see these entries in BibTeX format, use 'print(<citation>,
#> bibtex=TRUE)', 'toBibtex(.)', or set
#> 'options(citation.bibtex.max=999)'.

2 Quick start guide

2.1 Workflow