SQUID Python Suite (2023)
SQUID (Surrogate Quantitative Interpretability for Deepnets) is a Python suite to interpret sequence-based deep learning models for regulatory genomics data with domain-specific surrogate models. This software was developed in the Kinney lab and Koo lab at Cold Spring Harbor Laboratory.
For installation instructions, tutorials, and documentation, please refer to the SQUID website, https://squid-nn.readthedocs.io/. For an extended discussion of this approach and its applications, please refer to our manuscript.