Are there any citable Github repositories not published in journals, that receive a lot of citations? I wish to know whether there is some way, or maybe even some standard, for making a GitHub repository citable in a way that is recognized by academics. Many options have been suggested here, e.g., FigShare and Zenodo, but it seems to me that these routes are not actually established or taken seriously by academics.

For example, I made a Figshare DOI for my GitHub program in 2013 and it turned out to get zero citations, despite the paper related to the code getting many citations. People simply found citing something from Figshare to be awkward so the GitHub repository did not get citations the way an article would.

My question is this: Is there any practical evidence that some way of making a GitHub repository citable is somewhat accepted? For example, can anyone please point me to any GitHub repositories that have actually been cited many times as recognized by Google Scholar?
The Keras repository has an entry in Google Scholar with 1254 citations.

I'm not aware of the author having done anything special to make it "citable" though, other than giving an example in the FAQ of how to cite it.




  For example, I made a Figshare DOI for my GitHub program in 2013 and it turned out to get zero citations, despite the paper related to the code getting many citations.


Personally, whenever I wish to "cite a repository", the first thing I do is check the repository's homepage / documentation / FAQ / etc. to see if the author(s) wrote any instructions on how to cite it. If there are any such instructions, I use those since I assume that that is how the author(s) prefer to be cited.

If there are no such instructions, my next step is to see if there is any (peer-reviewed) paper published by the author(s) of the repository that describes / uses / links to the repository, and cite that if there exists such a thing. 

Only if there is no such paper do I consider directly citing the github link itself. The implicit assumption is that, unless there are explicit instructions stating otherwise, it is preferable to cite (peer-reviewed) papers over repositories.