This fall I took the course Mathematical Modelling of Football from Uppsala University. It was taught by Professor David Sumpter, and I believe this is the first academic course of its kind. The main subjects covered are modelling and analysis of events (on the ball actions), movement and pitch control (tracking data), player evaluation, and match result simulations. There were also several guest lectures from (among others) William Spearman, lead data scientist at Liverpool FC, and Javier Fernández, head of sports analytics at FC Barcelona.
The tools used were Python (using Anaconda) with NumPy, Pandas and Matplotlib. The course was a lot of work, especially the assignments, but I really enjoyed it and learned a lot.
Henrik Warne's blog 