CircleCI

📝 Note: This repository is the version of ABC presented in Gschwind et al. (BioRxiv 2023) and is a revamp of the original ABC codebase. To access any previous version of ABC, please visit https://github.com/EngreitzLab/ABC-Enhancer-Gene-Prediction-20250314-archive.

• For the version of ABC presented in Fulco et al. (Nat. Genet. 2019)[1], use the NG2019 branch of the archived repo
• For the version of ABC presented in Nasser et al. (Nature 2021), use the master branch of the archived repo

We have documented the codebase and usage in Read The Docs

Activity by Contact Model of Enhancer-Gene Specificity

The Activity-by-Contact (ABC) model predicts which enhancers regulate which genes on a cell type specific basis. This repository contains the code needed to run the ABC model as well as small sample data files, example commands, and some general tips and suggestions.

If you use the ABC model in published research, please cite:

[1] Fulco CP, Nasser J, Jones TR, Munson G, Bergman DT, Subramanian V, Grossman SR, Anyoha R, Doughty BR, Patwardhan TA, Nguyen TH, Kane M, Perez EM, Durand NC, Lareau CA, Stamenova EK, Aiden EL, Lander ES & Engreitz JM. Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations. Nat. Genet. 51, 1664–1669 (2019). https://www.nature.com/articles/s41588-019-0538-0

Contact

Please submit a GitHub issue with any questions or if you experience any issues/bugs.