Modeling Tutorials

Examples of applying SQUID on previously-published deep learning models can be found in the following Google Colab notebooks.

1. Colab – Additive (local) surrogate modeling with DeepSTARR

2. Colab – Pairwise (local) surrogate modeling with ResidualBind-32

3. Colab – Variant effect (local) prediction with DeepSTARR–Kipoi

Several Python examples are also provided in the SQUID repository.

1. Python – Variant effect (local) prediction with DeepSTARR–Kipoi

2. Python – Additive (global) surrogate modeling with BPNet–Kipoi

3. Python – Pairwise (global) surrogate modeling with BPNet–Kipoi

Note

While dependencies are automatically handled in the Colab notebooks, Python scripts must be run with the correct environment manually installed.