limix 1.0.18

A flexible and fast mixed model toolbox.

# Limix

[](https://pypi.python.org/pypi/limix/) [](https://pypi.python.org/pypi/limix/) [](https://anaconda.org/conda-forge/limix) [](https://limix.readthedocs.io/)

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 [conda](http://conda.pydata.org/docs/index.html) `bash conda install -c conda-forge limix `

An alternative way would be via pip `bash pip install limix `

In the second option, you will need to sort out some of its dependencies. At least the [liknorm](https://github.com/limix/liknorm) one.

## Problems

If you encounter any issue, please, [submit it](https://github.com/limix/limix/issues).

## Authors

• Christoph Lippert - [https://github.com/clippert](https://github.com/clippert)

• Danilo Horta - [https://github.com/Horta](https://github.com/Horta)

• Francesco Paolo Casale - [https://github.com/fpcasale](https://github.com/fpcasale)

• Oliver Stegle - [https://github.com/ostegle](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