Updates to R capstone from Melbourne sprint

Change summary:
 - Cleaned up some of the initial lesson code
 - Fixed consistency of variable naming and code comments
 - Added some additional teacher notes and explanations
 - Added missing data/counts.txt
   - Contents initially reconstructed from output in the analysis.md file
   - Spoofed differential RNAseq read counts so that:
      - analysis.Rmd can be knitr'd
      - generated plots are at least somewhat informative.