This project includes code from the following third-party projects. Each component retains its original license, which can be found in its respective directory.
- Directory:
alphagenome/ - Source: https://github.com/google-deepmind/alphagenome
- License: Apache License 2.0 (
alphagenome/LICENSE) - Copyright: Google DeepMind
AlphaGenome is used for variant effect prediction across multiple epigenomic layers. The code included in this repository is the official API client library and is unmodified.
- Directory:
ABC-FP/ - Source: https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction
- License: MIT License (
ABC-FP/LICENSE) - Copyright: 2020 Broad Institute
The Activity-by-Contact (ABC) model has been adapted to use TF footprinting data (ABC-FP-Max) for enhancer-gene linking predictions. Configuration files have been modified for use with FOODIE footprint data.