Python package for predicting single-cell CpG methylation states from DNA sequence and neighboring CpG sites using multi-task convolutional neural networks.

This repository is depracated. Please refer to the new DeepCpG package!.

The DeepCpG git repository can be checked out into the current directory by executing the command

git clone https://github.com/cangermueller/deepcpg.git.

To install DeepCpG, execute python setup.py install in the root directory.

DeepCpG builds upon a fork of the deep learning framework Keras, which can be installed by running the setup.sh script in the tools/ directory, which will checkout and install the repository.

The examples/ directory contains example scripts for training a small deep neural network and predicting missing methylation states afterwards. The necessary data sets can be downloaded by running data.sh. A network can be trained by running train.sh, and methylation states for a test data set be predicted by running predict.sh.

• /deepcpg/: DeepCpG package
• /script/: Scripts for data generation, model training, and imputation
• /examples/: Example files for model training and imputation
• /data/: Example data files

• Christof Angermueller
• [email protected]
• https://cangermueller.com