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

Plot gallery

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]. Exclude brackets if you don't use scanpy.

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

Changelog

0.3.0 (2020-06-03)

• Pandas helpers for easier normalization

0.2.0 (2020-06-03)

• Far faster implementation of stats.coclustering
• Introducing helpers.make_slurm_command
• Global submodule import (no longer need to import submodules individually)

0.1.0 (2020-03-06)

• First release on PyPI.