Efficient complex trait analyses from ARG
Project description
arg-lmm
This repository contains the source code for the ARG-RHE software for scalable variance component analysis using ancestral recombination graphs (ARGs), as well as other ARG-based linear mixed model analyses implemented in the ARG-LMM package. These methods are described in Zhu, Kalantzis et al., Cell Genomics, 2025.
For full usage guide, please refer to the arg-lmm manual. The source code, which relies on the arg-needle-lib library, is available in this repository. Additional scripts to reproduce the ARG-based linear mixed model analyses reported in Zhang et al., Nature Genetics, 2023 are available in this repository.
This package can be installed from PyPI, for example:
pip install arg-lmm
Licenses
The liu_sf method is copied from chiscore under MIT License instead of using PyPI due to a broken chi2comb dependency.
Citation
Zhu, Kalantzis, et al. (2025), "Fast variance component analysis using large-scale ancestral recombination graphs" https://doi.org/10.1101/2024.08.31.610262
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