General genetics/genomics utilities.
Project description
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:
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.
Project details
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