Linear mixed model for genomic analyses.
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README.md

Limix

PyPI-License PyPI-Version Anaconda-Server Badge 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.

⚠️ Note

Limix 2.0.0 is in the alpha stage but already functional. We thus recommend the user to first give it a try before using the stable version 1.0.x. Documentation and tutorials for 2.0.0 is already up and running.

Highlights

Install

The recommended way of installing it is via conda

conda install -c conda-forge limix

An alternative way would be via pip

pip install limix

In the second option, you will need to sort out some of its dependencies. At least the liknorm one.

Problems

If you encounter any issue, please, submit it.

Authors

License

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