We spend a lot of time to make our analyses reproducible. A review would allow us to collect some information on whether we are successful with 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.