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framework for developing sequence-level deep learning networks

Project description

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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 (or download the latest tagged version of Selene for a stable release):

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.

About Selene

Selene is composed of a command-line interface and an API (the selene-sdk Python package). Users supply their data, model architecture, and configuration parameters, and Selene runs the user-specified operations (training, evaluation, prediction) for that sequence-based model.

For a more detailed overview of the components in the Selene software development kit (SDK), please consult the page here.

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Tutorials and examples

Tutorials for selene are available here.

Documentation

The documentation for selene is available here.

Project details


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