``polyclonal`` documentation
===================================================

``polyclonal`` is a Python package for modeling mutational escape from polyclonal antibodies using deep mutational scanning data.

It is written by `the Bloom lab <https://jbloomlab.org>`_.

See `Yu et al (2022) <https://doi.org/10.1093/ve/veac110>`_ for an explanation of the approach implemented in ``polyclonal``.

See below for information and examples of how to use this package.

Contents
----------
.. toctree::
   :hidden:

   self

.. toctree::
   :maxdepth: 1

   installation
   biophysical_model
   visualize_RBD
   simulate_RBD
   fit_RBD
   fit_2epitope
   regularization
   RBD_average
   real_LyCoV1404
   reference_site_numbering
   real_cocktail
   specify_epitopes
   expt_design
   optimization
   partition_function
   polyclonal
   package_index
   acknowledgments