Chapter 4 Exploratory coverage analysis with superintronic and plyranges

Here we consider a tidy-data approach for exploring estimated coverage from RNA-seq data. We establish a simple framework, for aggregating across experimental design, and annotated genomic regions to discover ‘interesting’ coverage trace plots. We highlight how this framework can be used to develop data descriptions that find putative genes with intron retention. Our framework is implemented in a software package called superintronic, available at https://github.com/sa-lee/superintronic.