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1. process data 
preprocessData.R
2. use some classes 
useSomeClasses.R
3. balance data 
balanceSampleSize.R
4. train
trainModel.R
5. predict
predictModel.R
6. plot heatMap and paths 
plotCoefPath.R
plotCoefHeatMap.R
7. compute performance, change class labels
perform.R
testPerform.R
writePerformance.R
changeClassLabel.R
changeClassLabel2.R
8. write prediction to txt, color elements:   
writePrediction.R
getColorforElements.R
mergeRegions.R
9. main examples, cross-validation, and prediction
mainCV.R
visualization: to be finished

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R Tool for cis-Regulatory Element Prediction Version 1.0

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