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I'm using multimarkdown to write my thesis. It's a more advanced markdown parser which converts md to tex, and from there to pdf.
It's SO-NICE to write a thesis in markdown instead of having to think about styling and stuff at the same time.
A shoutout to the project, I'm happy with it
@freemo Mh, this could save me some time, instead of exporting graphs in R and calling them in MD I could just use Rmd. I'll give it a try, thanks!
Doc Freemo 
@arteteco Yea its pretty great for writing technical papers where you need some heavy hitting power but don't want the tedious nature of pdf EVERYWHERE.
I use it as a base for msot of my white papers.
@arteteco considering what your doing you might want to check out my own mrkdown to pdf code, it is similar advanced and allows you to add latex into the markdown.
https://jeffreyfreeman.me/latex-pdf-from-markdown/
I write a lot of technical documents, and it is important to me that they look nice. In the past I have always resorted to using latex directly....
jeffreyfreeman.me