I tried hard to make it reproducible, so hopefully this paper can serve as an example on how reproducibility can be achieved. I think that being reproducible with only few commands to type in a terminal is quite an achievment. At least in my field, where I usually see code published along with paper, but with almost no documentation on how to rerun it.
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.
It uses the drake R package that should make reproducibility of R projects much easier (just run make.R and you're done). However, it does depend on very specific package versions, which are provided by the accompanying docker image.
