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