genetools: single-cell analysis recipes (work in progress) codecov

Other features

  • Compare clustering results by computing co-clustering percentage.
  • Map marker genes against reference lists to find names for your clusters.
  • pandas shotrcuts:
    • Split single cell barcodes conveniently.
    • Defensive pandas merging and concatenation methods with strict correctness checks.

Full documentation:


Run pip install --upgrade 'genetools[scanpy]'.

Or if you don’t use scanpy: pip install --upgrade genetools.


To use genetools in a project, add import genetools. Review the documentation and the tests for examples.



git clone git://
cd genetools
pip install -r requirements_dev.txt
pre-commit install

Common commands:

# lint
make lint

# run tests
make test

# generate baseline figures (run from root directory)
make regen-tests

# bump version before submitting a PR against master (all master commits are deployed)
bump2version patch # possible: major / minor / patch

# also ensure updated


  • Main:
  • Docs: