framework for developing sequence-level deep learning networks
Project description
You have found Selene, a Python library and command line interface for training deep neural networks from biological sequence data such as genomes.
Installation
Selene is a Python 3+ package. We recommend using it with Python 3.6 or above.
Installing selene with Anaconda (for Linux):
conda install -c bioconda selene-sdk
Installing selene with pip:
pip install selene-sdk
Installing selene from source:
First, download the latest commits from the source repository:
git clone https://github.com/FunctionLab/selene.git
The setup.py
script requires NumPy. Please make sure you have this already installed.
If you plan on working in the selene
repository directly, we recommend setting up a conda environment using selene-cpu.yml
or selene-gpu.yml
(if CUDA is enabled on your machine) and activating it.
Selene contains some Cython files. You can build these by running
python setup.py build_ext --inplace
Otherwise, if you would like to locally install Selene, you can run
python setup.py install
Please install docopt
before running the command-line script selene_cli.py
provided in the repository.
Tutorials and examples
Tutorials for selene are available here.
Documentation
The documentation for selene is available here.
Project details
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