Introduction

This website is an attempt to collect all the tutoring information I've created and put it in one place that can be accessed from anywhere with an internet connection. Since it's all in one place instead of a variety of handouts, chapters can refer to one another, and it can be slightly more cohesive.

This isn't supposed to be a general or standalone course for either bioinformatics or R, but it isn't really a cookbook either. Instead, it's tailored for certain folks to do certain tasks, with an attempt to cut as straight a path there as possible while still giving enough information that said folks can be autonomous. Occasionally we'll need to make deviations learning about R rather than just strictly bioinformatics.

In general, it tries to assume you know little to no R. As such, it will probably seem to over-explain things to someone comfortable with R, or the code might not be written in the most succinct way. I think that's ok for now: we don't learn languages by reading - or writing - poetry.

If anything is confusing or if there is an area of particular interest, please let me know and I can do my best to clarify or include additional information.

Development

If you're interested in contributing to this book, the source code is located here.

It's built using soupault and the soupault book blueprint. As such, you'll need soupault.

Soupault doesn't have any kind of watch function to help with development, but you can kludge one together by running

find . | entr soupault

within the top level of the repository. If you're on macOS, you can get entr through Homebrew.

You'll probably also want to spin up an http server. If you have Python, you can do:

python3 -m http.server --directory build/

If you do contribute, I ask that you do not use any kind of LLM for your submission. In return, you can be assured that I will never use an LLM for any of these materials here. Thank you for understanding.