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General genetics/genomics utilities.

Project description

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

codecov

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]'.

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:

Changelog

0.4.0

  • Centered log ratio (CLR) normalization for Cite-seq protein data.

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.

Project details


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