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Framework for Interpretable Neural Networks for genetics
- What is GenNet?
- Getting started
- GenNet from command line.
- GenNet.py convert
- GenNet.py train
- GenNet.py plot
The Gennet framework is based on tensorflow, click here for the custom layer.
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GenNet uses CUDA. Please make sure you have the correct version of CUDA installed. GenNet has been tested for:
- CUDA 9.1 & Tensorflow 1.12.0
- CUDA 10.0 & Tensorflow 1.13.1
- CUDA 10.0 & Tensorflow 2.0.0-beta1
- CUDA 10.1 & Tensorflow 2.2.0
Open terminal. Navigate to the a place where you want to store the project. Clone the repository:
git clone https://github.com/arnovanhilten/GenNet
Navigate to the home folder and create a virtual environment
cd ~
python3 -m venv env_GenNet
This automatically instals the latest Tensorflow version for which GenNet has been tested. If you have an older version of CUDA install the appriopriate tensorflow-gpu by
pip install tensorflow-gpu==1.13.1
(change 1.13.1 to your version).
Activate the environment
source env_GenNet/bin/activate
Install the packages
pip3 install --upgrade pip
pip3 install -r requirements_GenNet.txt
Gennet is ready to use!
The command l
Open the command line and navigate to the GenNet folder
start the command line program by:
python GenNet.py
type --help for help
convert bed and vcf to .h5
Training the network
Generate plots