Writing a Data Science Book with Quarto (Using Jupyter Notebooks or Pandoc)

Summary

In the spirit of learning in public, I wanted an excuse to dive into Quarto to learn more about publishing formats beyond simple PDF and HTML documents. If you’re not familiar, Quarto (quarto.org) is the successor to RMarkdown, the next-generation scientific publishing system that works natively with Python, R, and OJS. If you already have RMarkdown you probably don’t have to do anything to it to get it to render with Quarto. The wonderful thing about Quarto (and to a lesser extent, RMarkdown) is that you can write one single input document and render many types of output documents — HTML, PDF, Word docs, presentations (Powerpoint, Beamer, RevealJS), dashboards, websites, books, blogs, and more). And, Quarto Live, you can embed WebAssembly-powered interactive code blocks for R and Python right into a Quarto document (example here). I demonstrate here how I turned an old course website of mine made from a bunch of RMarkdown documents into a polished e-book using Quarto. I also briefly point out Quarto Manuscripts and Quarto Dashboards at the end.You can read the book or download a PDF at https://bdsr.stephenturner.us/.Biological Data Science with RBack when I was faculty at UVA I started a series of workshops in response to the growing demand for practical education in data science and bioinformatics that the traditional coursework at the time lacked. I eventually turned this into a graduate course, and later into a course directed to faculty seeking a career in translational science. The course was a Software Carpentry style live coding hands-on course, mostly using R, that covered topics including data manipulation with dplyr, visualization with ggplot2, predictive modeling with caret, text mining with tidytext, RNA-seq analysis with DESeq2, basic statistics, survival analysis, and other topics. I made the course website using RMarkdown Websites — a feature that I don’t think ever got much traction, but I found incredibly useful. You put a _site.yml file in the roo...