molb-7950

Course materials for "MOLB 7950: Informatics and Statistics for Molecular Biology".

Installing local packages

pixi

Clone the repo, install pixi, then:

pixi install
pixi run install-pak-deps

This sets up R, Quarto, bioinformatics CLI tools, and all R packages. Packages not available on conda-forge/bioconda are installed via pak (see scripts/install-pak-deps.R).

To add a new package, either add it to pixi.toml (if on conda-forge/bioconda) or to scripts/install-pak-deps.R (if not), then commit pixi.lock.

Posit Cloud

Create a new template project and manually install packages with pak:

install.packages("pak")
pak::pak("tidyverse")

Previewing content

Use quarto render or quarto preview locally to inspect content prior to commit / push. A Github Action builds the site automatically unless you include [ci skip] in the commit message.

After a significant update (i.e., uploading a lot of class material), you should quarto render the entire site, and then commit & push the contents of the _freeze directory, which will enable rendering of only changed materials relative to that build.

File structure

Pages should be named based on the syllabus table, e.g., class-01.qmd.

The qmd files you want rendered as slides go in slides/, exercises/, problem-sets/, and problem-set-keys/

Each of these will be linked in the table on the front page.

If you want to suppress quarto rendering of a file, prefix the filename with an underscore like _class-01.qmd.

Syllabus updates

1. Edit the "Syllabus" sheet on the Google Sheet. Contact Jay if you need access.
2. Run data-raw/syllabus.R. You may be prompted to authenticate (one time). The writes a new data/syllabus.tsv file.
3. Re-render the page (quarto render index.qmd) and check formatting.
4. Commit and push to GitHub.

Additional, external content

• Problem sets and keys live here: https://github.com/rnabioco/molb-7950-problem-sets

• Large data sets, mainly single-cell problem sets, live here (so we don't bloat this repo): https://github.com/rnabioco/molb-7950-data/

AI tooling

Setup the project using the suggestions here: https://www.simonpcouch.com/blog/2025-07-17-claude-code-2/

Acknowledgements

This work borrows from and modifies: https://github.com/mine-cetinkaya-rundel/quarto-sdss