limix 1.0.0

A flexible and fast mixed model toolbox.

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) (public interface) (tutorial)

• mtSet: an efficient multi-trait set test (paper) (public interface) (tutorial)

Install

The recommended way of installing it is via pip

pip install limix

Problems

If you encounter any issue, please, submit it.

Authors

• Christoph Lippert - https://github.com/clippert

• Danilo Horta - https://github.com/Horta

• Franceso 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 file for details