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limix

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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. 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

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.

Limix software's Projects

ascertain icon ascertain

Statistics of variables under ascertainment

bgen icon bgen

A BGEN file format reader.

brent-search icon brent-search

Univariate function optimization based on Brent's method.

build-capi icon build-capi

Build and distribute C/C++ static libraries via Python packages.

cbgen icon cbgen

Python wrapper around bgen C library.

cellregmap icon cellregmap

CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq

chi2comb icon chi2comb

Linear combination of independent noncentral chi-squared random variables.

chi2comb-py icon chi2comb-py

Python package for linear combination of independent noncentral chi-squared random variables.

chiscore icon chiscore

Test statistics derived from linear combination of chi-squared distributions.

fast-lmm icon fast-lmm

Python version of Factored Spectrally Transformed Linear Mixed Models

glimix-core icon glimix-core

Fast inference for Generalised Linear Mixed Models.

hcephes icon hcephes

The Netlib Cephes library reformatted for the 21st century.

hgauss icon hgauss

Functions for Gaussian distribution.

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