I also got excited when I found out about R Markdown, and how well is integrated with RStudio. I believe that it is a decent alternative to Jypyter Notebook.
I would highly recommend GitLab for your use case. It is open source, it can be either on-prem or use their cloud offering, and features the GitLab Issues which is a neat issue tracker.
Very nice. I like the idea of this "HDK" as the post mentions. It would be useful in case that you want to conduct an experiment and use this HDK as your platform, and provide an easy way for others to fully understand your environment and test your results, eliminating any other factors.
In the same spirit, recently I found LittleFe [1]. I think it is now abandoned (based on the fact the the copyright message is still 2012 and the latest item in news was posted in March 2012), but it seems to be a good project.
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