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. You can also create a local copy of the API documentation by running:
make htmlin 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.
The quickest way to install Pyrepseq is via pip:
pip install pyrepseq[full]This will install pyrepseq with all optional dependencies. Depending on whether dependencies are already installed this might take a few minutes. You can also install the leading edge development version using:
pip install git+https://github.com/andim/pyrepseqAs the TCRdist dependency on parasail is known to cause installation issues on Mac OSX, pyrepseq can also be installed without this dependency by running:
pip install pyrepseqIn this case some functionality will not be available. To allow installation to proceed on mac you might have to manually install build tools using:
brew install autoconf automake libtoolPyrepseq can also be installed from its Github source, by running:
python setup.py installin 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.
Dependencies for generating testing and generating local versions of the documentation can be installed using:
pip install pyrepseq[dev]You are cordially invited to contribute to the further development of pyrepseq!