Accurate prediction of boundaries of high resolution

Kmer Research in Python and R

Data: 4mer, 6mer, 9mer and 12mer motif split from fruit fly DNA for TAD prediction.

Link to raw dataset: https://www.ncbi.nlm.nih.gov/gene?Db=gene&Cmd=DetailsSearch&Term=31358

Input:

Training csv file and testing csv file can be found in data folder.

Models:

Master_file.R is the combined master code for all of our working models used for feature based prediction.

Package Requirements: R Caret e1071 C5.0 Glmnet Python 3.6 Keras

All the feature-based machine learning models:

KNN
Decision Tree
Random Forest
Elastic Net Logistic Regression
Boosted Tree

Metrics recored:

Accuracy
Sensitivity
Specifitivity
F1 Score
AUC
Precision
Recall