Metadata-Version: 2.0
Name: limix
Version: 1.0.6
Summary: A flexible and fast mixed model toolbox.
Home-page: https://github.com/limix/limix
Author: Limix Developers
Author-email: horta@ebi.ac.uk
License: Apache License 2.0'
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Dist: scikit-learn
Requires-Dist: limix-core (>=1.0.1)
Requires-Dist: dask[bag,array,delayed,dataframe] (>=0.14)
Requires-Dist: h5py
Requires-Dist: pandas-plink (>=1.1.7)
Requires-Dist: limix-legacy
Requires-Dist: glimix-core (>=1.2.6)
Requires-Dist: joblib (>=0.11)
Requires-Dist: tqdm (>=4.10)
Requires-Dist: scipy (>=0.18)
Requires-Dist: distributed
Requires-Dist: numpy-sugar (>=1.0.38)
Requires-Dist: ncephes (>=1.0.37)
Requires-Dist: asciitree (>=0.3.3)

Limix
=====

|PyPI-License| |PyPI-Version| |Documentation Status|

Genomic analyses require flexible models that can be adapted to the
needs of the user. Limix is a flexible and efficient linear mixed model
library with interfaces to Python.

Limix includes methods for - single-variant association and interaction
testing, - variance decompostion analysis with linear mixed models, -
association and interaction set tests, - as well as different utils for
statistical analysis, basic i/o and plotting.

A description of the public interface is found at
https://limix.readthedocs.io/.

iPython notebook tutorials are available from github repository:
https://github.com/limix/limix-tutorials.

These tutorials can also be viewed using the ipython notebook viewer:
http://nbviewer.ipython.org/github/limix/limix-tutorials/blob/master/index.ipynb.

Highlights
^^^^^^^^^^

-  **iSet**: an interaction set test with external context
   (`paper <http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006693>`__)
   (`public interface <http://limix.readthedocs.io/iSet.html>`__)
   (`tutorial <https://github.com/limix/limix-tutorials/tree/master/iSet>`__)

-  **mtSet**: an efficient multi-trait set test
   (`paper <http://www.nature.com/nmeth/journal/v12/n8/abs/nmeth.3439.html>`__)
   (`public interface <http://limix.readthedocs.io/mtSet.html>`__)
   (`tutorial <https://github.com/limix/limix-tutorials/tree/master/mtSet>`__)

Install
-------

The recommended way of installing it is via
`pip <https://pypi.python.org/pypi/pip>`__

.. code:: bash

    pip install limix

Problems
--------

If you encounter any issue, please, `submit
it <https://github.com/limix/limix/issues>`__.

Authors
-------

-  **Christoph Lippert** - https://github.com/clippert
-  **Danilo Horta** - https://github.com/Horta
-  **Francesco Paolo Casale** - https://github.com/fpcasale
-  **Oliver Stegle** - https://github.com/ostegle

License
-------

This project is licensed under the Apache License (Version 2.0, January
2004) - see the `LICENSE <LICENSE>`__ file for details

.. |PyPI-License| image:: https://img.shields.io/pypi/l/limix.svg?style=flat-square
   :target: https://pypi.python.org/pypi/limix/
.. |PyPI-Version| image:: https://img.shields.io/pypi/v/limix.svg?style=flat-square
   :target: https://pypi.python.org/pypi/limix/
.. |Documentation Status| image:: https://readthedocs.org/projects/limix/badge/?style=flat-square&version=latest
   :target: https://limix.readthedocs.io/


