- The [*knitr*](http://cran.r-project.org/web/packages/knitr/index.html) package in R, for generating documents with R and markdown. For a n intro see [here](http://nicercode.github.io/guides/reports/)
- version control via git (see next section)
- JAGS - Just another Gibbs Sampler. Install [here](http://sourceforge.net/projects/mcmc-jags/files/)