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

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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: https://genetools.maximz.com.

Install

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

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

Usage

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

Development

Setup:

git clone git://github.com/maximz/genetools
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 CHANGELOG.md updated

CI:

  • Main: https://travis-ci.com/github/maximz/genetools
  • Docs: https://app.netlify.com/sites/genetools