Metadata-Version: 2.1
Name: genetools
Version: 0.2.0
Summary: General genetics/genomics utilities.
Home-page: https://github.com/maximz/genetools
Author: Maxim Zaslavsky
Author-email: maxim@maximz.com
License: MIT license
Description: # genetools: single-cell analysis recipes (work in progress)
        
        ![https://pypi.python.org/pypi/genetools](https://img.shields.io/pypi/v/genetools.svg)
        ![https://travis-ci.com/maximz/genetools](https://img.shields.io/travis/maximz/genetools.svg)
        
        ## Plot gallery
        
        <table>
        <tr>
        <td>
        
        [![](tests/baseline/test_umap_scatter_discrete.png)](https://github.com/maximz/genetools/blob/master/tests/test_plots.py)
        
        </td>
        <td>
        
        [![](tests/baseline/test_horizontal_stacked_bar_plot.png)](https://github.com/maximz/genetools/blob/master/tests/test_plots.py)
        
        </td>
        </tr>
        </table>
        
        ## 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](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](https://genetools.maximz.com) and the [tests](https://github.com/maximz/genetools/tree/master/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
        
        ## 0.2.0 (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.
        
Keywords: genetools
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: scanpy
