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FaST-LMM

FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed Models, is a program for performing genome-wide association studies (GWAS) on datasets of all sizes, up to one millions samples.

This release contains the following features, each illustrated with an IPython notebook.

Improvements:

A C++ version, which is generally less functional, is available. See http://fastlmm.github.io/.

Quick install:

pip install fastlmm

If you need support for BGEN files, instead do:

pip install fastlmm[bgen]

For best performance, be sure your Python distribution includes a fast version of NumPy. We use Anaconda's Miniconda.

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Code

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