Tools & Workflows

An overview of the tools and workflows I use for research, teaching, and coding

I learn a lot from other people sharing the tools and workflows they use. So here I want to share my own list. This is a snapshot of what I currently use for research, teaching and coding. Still far from perfect, and always changing as I find better ways to work, but here it is.

Coding & analysis

I work mostly in R (data analysis, modelling, workflow automation). But I’ve also dabbled in Python and C++, and learning Julia is next on my list, since it’s increasingly popular for modelling.

My main editor is Positron because it is built for R and data science but I keep the flexibility I had coming from VS Code. In Positron, I can work across languages in one project and the R setup just works out of the box. I enjoy all the small features: A nice Git GUI, side-by-side file layout, a CSV viewer with summaries for each column, a PNG viewer that updates when I rerun the plot code, and many more.

For teaching, I still really like and use RStudio though because of how robust and intuitive it is.

Some R packages I use regularly (there are too many to list them all so here are my favourites):

  • tidyverse: My default for everything data-analysis related. I like how well all the tidyverse packages work together and how intuitive it is, which is especially great for teaching.
  • patchwork: My favourite ggplot2 extension package to combine multiple plots into one
  • usethis: A workflow package I use to build R packages, and to manage the Git and GitHub setup in my projects.
  • reprex: I use it to create reproducible examples to make sure code is self-contained and actually runs on someone else’s machine.
  • For fast data analysis and bigger datasets, I like to use data.table and collapse, and furrr for parallelisation.

For version control I use Git and mostly GitHub, mainly through the editor or the terminal. For teaching, I switch to GitHub Desktop though because it is more intuitive for people new to version control.

Notes & knowledge

Obsidian is one of my most-used applications. I use it for everything from quick notes, to-do lists, planning workshops and papers, collecting literature and ideas. What I like most is that Obsidian notes are plain Markdown files which means they are future-proof, portable and not locked into any proprietary file formats. I also really enjoy the extension ecosystem and building my own workflows in Obsidian. It’s a rabbit hole I occasionally disappear into.

Writing & References

I write in Google Docs when collaborating with others and in Obsidian for my own drafts.

I manage literature references with Zotero and Obsidian. I read and annotate papers in Zotero on an iPad, sync to my computer, and then turn each paper into a structured literature note in Obsidian.

Web & Media

I build my workshop and personal websites with Quarto, version controlled on GitHub and deployed via GitHub pages or Netlify (like this page here).

I use OBS for screen and video recording and DaVinci Resolve for editing videos, workshop recordings and tutorials.

AI

I am genuinely conflicted about AI tools. I mainly use Claude Code for feedback and improvement suggestions on my code and for learning new coding methods. I try to use AI tools only in areas where I know enough to judge the quality of the answer and try not to outsource my own thinking to AI. But this is a very fine line that is easy to cross sometimes. I also use Claude for general questions or feedback on my ideas.

OS

Regarding operating systems, I am on Windows, mostly so I can help others in our lab with their setups. But I would like to switch and try Linux.