A very common task in bioinformatics is writing up our results in order to communicate them to a colleague or just to have a good record in our laboratory books (electronic or otherwise). A key skill is to make the work as reproducible as possible so that we can rerun it ourselves when we need to revisit it or someone else interested in what we did can replicate the process. One increasingly popular solution to this problem is to use literate programming techniques and executable notebooks that are a mixture of human-readable text, analytical code, and computational output rolled into a single document. In R, the rmarkdown package allows us to combine code and text in this way and create output documents in a variety of formats.

In this recipe, we'll look at the large-scale structure of one such document that can be compiled with rmarkdown. The RStudio application makes this process very straightforward so we'll look at compilation from within that tool.