gDNAx: Diagnostics for assessing genomic DNA contamination in RNA-seq data

Current Bioconductor build status

• release
• development

The gDNAx package calculates and plots different diagnostics related to gDNA contamination levels, such as strandedness and proportion of intergenic reads, intronic reads, splice compatible exonic reads and splice compatible junction reads. Moreover, the package is able to identify the strand library type in stranded RNA-seq data.

Installation

You can install the gDNAx package from this GitHub repo using the remotes package, as follows:

library(remotes)

install_github("rcastelo/gDNAx")

Provided that you have installed first all its Bioconductor dependencies; see the DESCRIPTION file. The vignette contains an example on how to use it.

Questions, bug reports and issues

For bug reports and issues regarding this development version of gDNAx please use the GitHub issues tab at the top-left of this page.

Contributing

Contributions to the software codebase of gDNAx are welcome as long as contributors abide to the terms of the Bioconductor Contributor Code of Conduct. If you want to contribute to the development of gDNAx please open an issue to start discussing your suggestion or, in case of a bugfix or a straightforward feature, directly a pull request.

Funding

This software project is supported in part by the Spanish Ministry of Science, Innovation and Universities.