GaugeFixer is a lightweight Python package that allows interpretation of the parameters of linear models for sequence-function relationships by removing unconstrained degrees of freedom in their values, an operation known as "fixing the gauge".
Create a new python environment with conda and activate it
conda create -n gaugefixer python=3.10
conda activate gaugefixerInstall the latest stable from PyPI using the pip package manager
pip install gaugefixerOnline documentation is available at readthedocs
Download the lastest version from GitHub
git clone https://github.com/jbkinney/gaugefixer.gitand install the package in development model
pip install -e gaugefixerRun tests with:
pytest test To build the documentation of the package:
cd docs
pip install -r requirements.txt
bash build_docs.shSee the LICENSE file for details.
Carlos Martí-Gómez, David M. McCandlish, Justin B. Kinney (2025). GaugeFixer: Removing unconstrained degrees of freedom in sequence-function relationships. bioRxiv.