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.
Because: - Two fellow PhDs working on different topics have been able to reproduce some figures by following the README instructions and I hope this extends to other people - I've tried to incorporate as many of the best practices as possible to make my code and data open and accessible - I've tried to make sure that my data is exactly reproducible with the specified random seed strategy - the paper suggests a method that should be useful to other researchers in my field, which is not useful unless my results are reproducible
I tried hard to make this paper as reproducible as possible, but as techniques and dependencies become more complex, it is hard to make it 100% clear. Any form of feedback is more than welcome.
The original data took quite a while to produce for a previous paper, but for this paper, all tables and figures should be exactly reproducible by simply running the jupyter notebook.