Enhancer Activity Predictor is an R script that uses combinatorial TF ChIP scores as input to predict enhancer activity.
In order to download Enhancer Activity Predictor, clone the repository via the following commands
git clone https://github.com/UIUCSinhaLab/Enhancer-Activity-Predictor
cd Enhancer-Activity-Predictor
R >= 3.3.0
R packages: xgboost, DMwR
CAD4DmelEnhancers.txt has 232 D. melanogaster enhancers. Columns are putative enhancer coordinates and ID, experimentally verified enhancer coordiates and ID, Mesoderm activity, Visceral Muscle activity, Somatic Muscle activity, and 14 D. melanogaster ChIP scores at specific TF:Time_Point condition.
DmelOrthChIP.txt is a sample input file for enhancer activity prediction. Columns 1-14 are TF-ChIP scores for D. melanogaster, and columns 15-28 are TF-ChIP scores for D. virilis.
If you use the R script or the enhancer activity data, please cite this paper. Peng, Pei-Chen, et al. "The role of chromatin accessibility in cis-regulatory evolution." Genome biology and evolution 11.7 (2019): 1813-1828.