Genetic analysis toolbox using mixed models
Project description
limix
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. It includes methods for
- Single-variant association and interaction testing
- Variance decompostion analysis with linear mixed models
- Association and interaction set tests
- Different utils for statistical analysis, basic i/o, and plotting.
We have an extensive documentation of the library. If you need further help or want to discuss anything related to limix, please, join our forum 💬 and have a chat with us 😃. In case you have found a bug, please, report it creating an issue.
Install
NOTE: We will be maintaining limix 2.0.x for a while, in case you find some missing feature in limix 3.0.x. If that is the case, please, type
pip install "limix <3,>=2"in your terminal.
Installation is easy and works on macOS, Linux, and Windows:
pip install limix
If you already have Limix but want to upgrade it to the latest version:
pip install limix --upgrade
Interactive tutorials
- eQTL (requires limix 2.0.x)
- Struct-LMM (requires limix 2.0.x)
Running tests
After installation, you can test it
python -c "import limix; limix.test()"
as long as you have pytest.
Authors
License
This project is licensed under the Apache License License.
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