Repeat the analyses on 20190115

This is a fresh run of the Rmd files using a current revision of hpgltools.

I know what year it is, honest.

I messed up the date in the first release, I also had some spurious contrasts included.

Initial analysis release

In this release I just reran my previous copy of the analyses with hopefully no changes, but to try and make sure that the code still works since I first did it a year ago.

I am thinking it would be good to include some IGV pictures and maybe some of our other metrics to show the usability of the samples.