https://github.com/shz9/magenpy

Modeling and Analysis of (Statistical) Genetics data in python
https://github.com/shz9/magenpy

genotype gwas ldsc linkage-disequilibrium phenotype prs simulation

Last synced: 22 days ago
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Modeling and Analysis of (Statistical) Genetics data in python

• Host: GitHub
• URL: https://github.com/shz9/magenpy
• Owner: shz9
• License: mit
• Created: 2020-08-03T04:43:34.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2026-06-30T17:27:37.000Z (23 days ago)
• Last Synced: 2026-06-30T18:13:05.147Z (23 days ago)
• Topics: genotype, gwas, ldsc, linkage-disequilibrium, phenotype, prs, simulation
• Language: Python
• Homepage: https://shz9.github.io/magenpy/
• Size: 2.59 MB
• Stars: 19
• Watchers: 1
• Forks: 6
• Open Issues: 7
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE
  • Citation: CITATION.md

Awesome Lists containing this project

• awesome-complex-trait-genetics - magenpy - based library that provides utilities for simulating complex traits with various genetic architectures. (Simulation / Mendelian randomization in _cis_)

README

          
# `magenpy`: *M*odeling and *A*nalysis of (Statistical) *Gen*etics data in *py*thon

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`magenpy` is a Python package for modeling and analyzing statistical genetics data. 

The package provides tools for:

* Reading and processing genotype data in `plink` BED format.

* Efficient LD matrix construction and storage in [Zarr](https://zarr.readthedocs.io/en/stable/index.html) array format.

* Data structures for harmonizing various GWAS data sources.

  * Includes parsers for commonly used GWAS summary statistics formats.

* Simulating polygenic traits (continuous and binary) using complex genetic architectures.

    * Multi-cohort simulation scenarios (beta)

    * Simulations incorporating functional annotations in the genetic architecture (beta)

* Interfaces for performing association testing on simulated and real phenotypes.

* Preliminary support for processing and integrating genomic annotations with other data sources.

### Helpful links

- [Documentation](https://shz9.github.io/magenpy/)

- [Citation / BibTeX records](./CITATION.md)

- [Report issues/bugs](https://github.com/shz9/magenpy/issues)

### AI Usage

[![AI-DECLARATION: assist](https://img.shields.io/badge/䷼%20AI--DECLARATION-assist-fef9c3?labelColor=fef9c3)](https://ai-declaration.md)

This project is developed using AI-assisted technologies. Please review our [AI Declaration](AI-DECLARATION.md) for full transparency on automated pipelines.