GitHub - yifeng-li/cis-reg_v1_0: R Tool for cis-Regulatory Element Prediction Version 1.0

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R Tool for cis-Regulatory Element Prediction Version 1.0

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Name		Name	Last commit message	Last commit date
Latest commit History 1 Commit
balanceSampleSize.R		balanceSampleSize.R
changeClassLabel.R		changeClassLabel.R
changeClassLabel2.R		changeClassLabel2.R
getColorforElements.R		getColorforElements.R
logTransform.R		logTransform.R
mainCV.R		mainCV.R
meanPerform.R		meanPerform.R
mergeRegions.R		mergeRegions.R
perform.R		perform.R
plotCoefHeatMap.R		plotCoefHeatMap.R
plotCoefPath.R		plotCoefPath.R
predictModel.R		predictModel.R
preprocessData.R		preprocessData.R
readme.txt		readme.txt
stdCol.R		stdCol.R
sumCol.R		sumCol.R
testPerform.R		testPerform.R
trainModel.R		trainModel.R
useSomeClasses.R		useSomeClasses.R
writePerformance.R		writePerformance.R
writePrediction.R		writePrediction.R

Repository files navigation

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