Two command line tools (Neural network and simple interpolation) for restoring missing areas in Hi-C maps
Simple interpolation model:
python3 neural_network.py PATH_TO_YOUR_COOL_FILE [DEFECT_THRESHOLD]
Neural network model:
python3 interpolation.py PATH_TO_YOUR_COOL_FILE [DEFECT_THRESHOLD]
DEFECT_THRESHOLD is an optional argument which defines minimal percent of non-zero values in row/column for this row/column to be valid. By default DEFECT_THRESHOLD is set to 5%.