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[full]

This will install pyrepseq with all optional dependencies (TCRdist and SCEPTR support are optional). 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/pyrepseq

As 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 pyrepseq

In 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 libtool

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. 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!