I do all of my analysis in R. I will post useful code on this page and on Github from time to time.

 

Code:

Coming soon

 

Nice Links

BRAD: http://brassicadb.org/brad/

R: http://cran.r-project.org/

R package PopGenome: http://cran.r-project.org/web/packages/PopGenome/index.html

R graphics: http://cran.r-project.org/web/packages/ggplot2/index.html

UCSC Genome Browser: http://genome.ucsc.edu/

IPlant: http://www.iplantcollaborative.org/

Handbook of Biological Statistics: http://www.biostathandbook.com/