Are there any citable Github repositories not published in journals, that receive a lot of citations?
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.