Above diagram from Emmert-Streib, Moutari, and Dehmer (2016) nicely depicts how “data science” takes a combination of three kinds of disciplines. It can be a bit daunting to expand our expertise away from our home vertex. I was fortunate to be in a great training environment: my supervisor and the Howard Hughes Medical Institute sponsored me to attend the advanced sequencing technolgies/bioinformatics course at Cold Spring Harbor Labs, and senior graduate students organized bioinformatics workshops. It’s not that these two taught me everything I know about bioinformatics now; they got the ball rolling in a really good direction.
So I guess I should pay it forward. To whom? I’m not sure. I threw some stuff on RNA-seq together in 2023 for trainees on the 4th floor VRL—a pilot run, and attendance took a nose dive after the second week. A big problem (among many others) was copying and pasting my code from Powerpoint text boxes. Sometimes there would be a new line character error. Since then, I learned about HTML slides with xaringan or Quarto revealjs that have native code block support 🥳.
Links to my slides are on my github pages1. The goal of this series is to demonstrate a RNA-seq workflow from Illumina reads to plots (PCA, Volcano, heatmap). At the time of writing, there are three weeks (one hour session each) worth of material. Week 1 slides are shown below as a teaser.
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References
Footnotes
I think this is a cute hack because a repo is meant to host just one presentation. But I wanted to have all slides in one repo. In the
docsdirectory in the top directory of my repo, I made a Quarto website (qmd) rendered to html. I got rid of the defaultindex.htmlthat just redirects to the slides. Github pages serves this html instead of redirecting. I tried to add a_quarto.ymlto this index file, but it seemed to destroy the rendering.↩︎embedioextension used to embed these slides↩︎