Python library for immune repertoire analyses
Project description
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. 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.
Installation
The quickest way to install Pyrepseq is via pip:
pip install pyrepseq
Pyrepseq can also be installed from its Github 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, or (even better!) open a pull request with relevant changes. If you have any questions don't hesitate to contact us by email (andimscience@gmail.com) or Twitter (@andimscience).
You can run the testsuite by running pytest in the top-level directory.
You are cordially invited to contribute to the further development of pyrepseq!
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