limix/geno-sugar

Utilities for handling genetic data for GWAS

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

• Christoph Lippert
• Danilo Horta
• Francesco Paolo Casale
• Oliver Stegle

License

This project is licensed under the Apache License License.

geno-sugar's Issues

Support bgen

Add support and examples from bgen genotypes imported using the bgen reader

struct_lmm utils not installed

I have installed struct_lmm using pip but the "utils" subdirectory is not installed so I cannot import the run_structlmm or norm_env_matrix items. Please advise next steps. Thank you!