acdc-exploratory-analysis

Exploratory analysis of ACDC clinical data pulled from the Gen3 commons via the gen3-metadata package. Notebooks are authored with marimo for interactive, reproducible exploration.

Quickstart

# install dependencies
poetry install

# launch the exploratory notebook
poetry run marimo edit notebooks/exploratory.py

You will need a Gen3 credentials JSON file. Place it outside the repo (or somewhere that is gitignored) and update the key_file path in the first cell of the notebook.

Layout

• notebooks/exploratory.py — marimo notebook; first cell fetches ACDC metadata.
• pyproject.toml — Poetry-managed dependencies (marimo, gen3-metadata==1.4.0, pandas).

To export to html

DATETIME=$(date +%Y%m%d_%H%M%S)
poetry run marimo export html --no-include-code notebooks/pipeline.py -o outputs/${DATETIME}_acdc_exploratory_analysis.html