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.

See Yu et al (2022) for an explanation of the approach implemented in polyclonal.

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

Contents

• Installation
• Biophysical model
• Visualize antibody mix
• Simulate experiment
• Fit model to data
• Fit more complex curves
• Regularization
• Averaging models
• Real antibody example
• Reference site numbering
• Real antibody cocktail
• Specifying epitopes
• Experimental design
• Details on fitting
• Distinct epitopes assumption
• polyclonal package
• package index
• Acknowledgements