I used a fork of a GitHub repository whose paper I cited – should I also cite the fork? I want to cite a GitHub repository in scientific publications.
The repository that I used is a fork version of the original GitHub repository which is accompanied by a paper.
Both repositories are the same, but the fork has additional code for further calculations and plots. 

I cited the paper to refer to the methodology.
But I did not use the original GitHub provided by the paper. Instead, I used the fork.

Should I cite the fork?
You should cite the original paper and the GitHub fork.  You are obligated to cite all sources you used, even if they overlap.  Your methods should also state exactly what code you reused.