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Tutorials

These tutorials cover compute and report workflows. Each one has a matching Jupyter notebook under the repository’s notebooks/ directory, but the commands shown here can also be run directly in a shell.

Notebook Setup

Install the CLI from the checkout:

cargo install --path /path/to/genesets-rs --force

Install the workflow/notebook environment from the Python package:

uv run --project python/genesets-workflows --extra notebooks genesets-workflows doctor

Generated notebook outputs should be written under notebooks/generated/, which is ignored by git.

Available Tutorials

  • CLI Quickstart: run the bundled example and inspect the enrichment TSV.
  • Expression20 vs GO: enrich the small expression-derived panel against official GOA human/GO targets.
  • GO Impact Report: compare 2021 vs 2026 GO/GOA over 500 expression-derived gene sets using a parameterized report config, then inspect threshold crossings and timings.