Is it ok to use Github code by having explicit permission from author for Thesis but without license mentioned on the repository?
There are both legal and academic aspects to this. The the single most operative question here being &quot;permission to do what?&quot;:

If your thesis quotes significant portions of the original code then you need permission to reproduce it (very small portions are likely to be covered by whatever fair use/fair dealing defence the relevant jurisdictions allow).
If you are distributing the code online (e.g. by creating a public GitHub fork with your modifications in it) then you also need permission to distribute it.
If you are expecting your changes to be used and modified by others (which is generally thought of as a good thing for both knowledge and reproducible code), then you probably want to release it to them under a specific licence yourself, for which you will again want the permission of the original author.

All together, if you are literally only citing the code (e.g. &quot;Plots were created with a modified version of Library X [https://github.com/foo/libraryX] under special licence from the author.&quot; ), then you don't need to do anything more. If you want your work to be useful to others in the future, then you should encourage the author to pick a licence and update their repository, then do the same with your version.