Adapt to the new MTP-DB

[MrHedmad]

The MTP-DB is about to update. This PR adapts the analysis to the new features of the MTP-DB.

As of PR creation, the changes are as follow:

• Used the sources table in the generation of the genesets;
• Updated the default pruning threshold to something more sensible;
• Fixed issue https://github.com/CMA-Lab/MTP-DB/issues/25 (which is in the wrong repo, anyway. Who did this!?)
• Added a cleaner way to remake the paper without running the whole analysis, just make thin_paper.
• Updated the README slightly.

This is still a draft! Merging before https://github.com/CMA-Lab/MTP-DB/pull/41 will break stuff!