Using Markdown and Quarto for literate computation
A very common task in bioinformatics is writing up our results in order to communicate them to colleagues or 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 when someone else needs to replicate the process. One very popular way to solve 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 R Markdown extension of the Markdown syntax and the Quarto command-line tool (and R package) allow 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 a typical document that can be rendered into multiple formats with Quarto.