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+# maui
+
+[![Downloads](https://pepy.tech/badge/maui-tools)](https://pepy.tech/project/maui-tools)  [![codecov](https://codecov.io/gh/bimsbbioinfo/maui/branch/master/graph/badge.svg)](https://codecov.io/gh/bimsbbioinfo/maui) [![Codacy Badge](https://api.codacy.com/project/badge/Grade/36c1f3f252b543139fd930ba5f674535)](https://www.codacy.com/app/jonathanronen/maui?utm_source=github.com&utm_medium=referral&utm_content=BIMSBbioinfo/maui&utm_campaign=Badge_Grade) [![PyPI version](https://badge.fury.io/py/maui-tools.svg)](https://badge.fury.io/py/maui-tools) [![Documentation Status](https://readthedocs.org/projects/maui/badge/?version=latest)](https://maui.readthedocs.io/en/latest/?badge=latest) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
+
+
+
+<!-- [![Build Status](https://travis-ci.com/BIMSBbioinfo/maui.svg?branch=master)](https://travis-ci.com/BIMSBbioinfo/maui) -->
+
+
+Multi-omics Autoencoder Integration (**maui**) is a python package for multi-omics data analysis. It is based on a bayesian latent factor model, with inference done using artificial neural networks. For details, check out our LSA paper: https://www.life-science-alliance.org/content/2/6/e201900517
+
+## Installation
+
+maui works with Python 3.6 and TensorFlow 1.1 (does not yet support the yet unreleased TensorFlow 2.0). The easiest way to install is from pypi:
+
+	pip install -U maui-tools
+
+This will install all necessary dependencies including keras an tensorflow. The default tensorflow (cpu) will be installed. If tensorflow GPU is needed, please install it prior to installation of maui.
+
+The development version may be installed by cloning this repo and running `python setup.py install`, or, using `pip` directly from github:
+
+	pip install -e git+https://github.com/BIMSBbioinfo/maui.git#egg=maui
+
+
+#### Optional dependencies
+
+Survival analysis functionality supplied by lifelines [1]. It may be installed directly from pip using `pip install lifelines`.
+
+## Usage
+
+See [the vignette](vignette/maui_vignette.ipynb), and check out [the documentation](https://maui.readthedocs.io/en/latest/).
+
+
+## Citation
+
+>  Evaluation of colorectal cancer subtypes and cell lines using deep learning. Jonathan Ronen, Sikander Hayat, Altuna Akalin. Life Science Alliance Dec 2019, 2 (6) e201900517; DOI: 10.26508/lsa.201900517
+
+## Contributing
+
+Open an issue, send us a pull request, or shoot us an e-mail.
+
+## License
+
+maui is released under the [GNU General Public License v3.0](LICENSE) or later.
+
+---------------------
+@jonathanronen, BIMSBbioinfo, 2018
+
+
+[1]: https://github.com/CamDavidsonPilon/lifelines