I tried as hard as possible to make it reproducible, which it is on my computer. I would be happy to see if this still works on other computers. Moreover, by allowing easy reproducibility, I hope that other people may easily build research on top of this work.
The code and data are both on GitHub. The paper has been published in Wellcome Open Research and has been replicated by multiple other authors.
Metadata annotation is key to reproducibility in sequencing experiments. Reproducing this research using the scripts provided will also show the current level of annotation in years since 2015 when the paper was published.