📝 Note: This is an archived copy of the ABC codebase from https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction with full commit history, saved on 03/14/2025. Only use this backup to access outdated branches of ABC, including the master branch which was used in [1]. For the active and maintained ABC repo, please visit https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction.
We have documented the codebase and usage in Read The Docs
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