Pyrepseq is scipy & seaborn for studying adaptive immunity: modular implementations of algorithms for fast analyses, and bespoke plotting functions for compelling visualizations.
You can find API documentation on readthedocs
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.
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.
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!