Metadata-Version: 2.1
Name: scvi
Version: 0.1.2
Summary: Single-cell Variational Inference
Home-page: https://github.com/YosefLab/scVI
Author: Romain Lopez, Jeffrey Regier, Maxime Langevin, Edouard Mehlman, Yining Liu
Author-email: romain_lopez@berkeley.edu
License: MIT license
Keywords: scvi
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.6
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: numpy (>=1.0)
Requires-Dist: torch (>=0.4)
Requires-Dist: matplotlib (>=2.0)
Requires-Dist: scikit-learn (>=0.18)
Requires-Dist: scipy (>=1.0)
Requires-Dist: h5py (>=2.8)
Requires-Dist: pandas (>=0.2)
Requires-Dist: loompy (>=2.0)

====
scVI
====

.. image:: https://travis-ci.org/YosefLab/scVI.svg?branch=master
    :target: https://travis-ci.org/YosefLab/scVI

.. image:: https://codecov.io/gh/YosefLab/scVI/branch/master/graph/badge.svg
  :target: https://codecov.io/gh/YosefLab/scVI

.. image:: https://readthedocs.org/projects/scvi/badge/?version=latest
        :target: https://scvi.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status


Single-cell Variational Inference


* Free software: MIT license
* Documentation: https://scvi.readthedocs.io.


Installation
--------

1. Install PyTorch: http://pytorch.org

2. Install this repository from source: ``git clone https://github.com/YosefLab/scVI.git``

3. Refer to the examples_ subdirectory for Jupyter notebooks that illustrate usage. 

.. _examples: https://github.com/YosefLab/scVI/tree/master/examples

Benchmarks
--------

To recreate the results appearing in the paper referenced below, run

.. code-block::

    python ./run_benchmarks.py --dataset=cortex 

References
--------

Romain Lopez, Jeffrey Regier, Michael B Cole, Michael Jordan, Nir Yosef.
**"Bayesian Inference for a Generative Model of Transcriptome Profiles from Single-cell RNA Sequencing."**
In submission. Preprint available at https://www.biorxiv.org/content/early/2018/03/30/292037


=======
History
=======

0.1.0 (2018-06-12)
0.1.1 (2018-06-14)
0.1.2 (2018-06-16)
------------------

* First release on PyPI.


