CircleCI
📝 Note: This is a revamp of the ABC codebase presented in [1]. If you wish to access that version of the ABC repo, please check out https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/tree/master.
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
Please submit a github issue with any questions or if you experience any issues/bugs.