Here I scaned all PubMed Central (PMC) free papers for github links. I descovered 65366 articles with links to 58255 repositories. Summary information about papers (pmc id, publication year, keywords, title) and repositories (including language usage statistics) are provided in rds files.
iaaka/bioinf.lang.stat
Analysis of programming languages used in github repositories mentioned in free PMC papers
Jupyter Notebook