Metadata-Version: 2.1
Name: pyrepseq
Version: 1.4.2
Summary: Python library for immune repertoire analyses
Home-page: http://pyrepseq.readthedocs.io/
Download-URL: http://github.com/andim/pyrepseq
Author: Q-Immuno Lab (PI: Andreas Tiffeau-Mayer)
Author-email: qimmuno@gmail.com
Maintainer: Andreas Tiffeau-Mayer
Maintainer-email: andimscience@gmail.com
License: MIT
Platform: OS Independent
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: pandas
Requires-Dist: rapidfuzz
Requires-Dist: Levenshtein
Requires-Dist: matplotlib
Requires-Dist: seaborn
Requires-Dist: igraph
Requires-Dist: scikit-learn
Requires-Dist: logomaker
Requires-Dist: biopython
Requires-Dist: tcrdist3
Requires-Dist: tidytcells ~=2.0
Provides-Extra: dev
Requires-Dist: pytest ; extra == 'dev'
Requires-Dist: pytest-cov ; extra == 'dev'
Requires-Dist: sphinx ; extra == 'dev'
Requires-Dist: sphinx-rtd-theme ; extra == 'dev'

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# Pyrepseq: the immune repertoire analysis toolkit

Pyrepseq is `scipy` & `seaborn` for studying adaptive immunity: modular implementations of algorithms for fast analyses, and bespoke plotting functions for compelling visualizations.

## Documentation and examples

You can find API documentation on [readthedocs](https://pyrepseq.readthedocs.io/en/latest/?badge=latest). You can also create a local copy of the API documentation by running `make html` in the docs folder.

There are jupyter notebooks illustrating some of the functionality in the 'examples' folder.

You can also find usage examples by looking at the code underlying our recent paper [Mayer Callan PNAS 2023](https://github.com/andim/paper_coincidences).

## Installation

The quickest way to install Pyrepseq is via pip:

`pip install pyrepseq`


Pyrepseq can also be installed from its [Github](https://github.com/andim/pyrepseq) source, by running `python setup.py install` in the main directory.

## Support and contributing

For bug reports and enhancement requests use the [Github issue tool](http://github.com/andim/pyrepseq/issues/new), or (even better!) open a [pull request](http://github.com/andim/pyrepseq/pulls) with relevant changes. If you have any questions don't hesitate to contact us by email (andimscience@gmail.com) or Twitter ([@andimscience](http://twitter.com/andimscience)).

You can run the testsuite by running `pytest` in the top-level directory.

You are cordially invited to [contribute](https://github.com/andim/pyrepseq/blob/master/CONTRIBUTING.md) to the further development of pyrepseq!
