A flexible and fast mixed model toolbox.
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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.
- 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))
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.
If you encounter any issue, please, [submit it](https://github.com/limix/limix/issues).
- 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)
This project is licensed under the Apache License (Version 2.0, January 2004) - see the [LICENSE](LICENSE) file for details