Modeling and Analysis of Statistical Genetics data in python

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  • Author: Shadi Zabad
  • Requires: Python >=3.8
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magenpy: Modeling and Analysis of (Statistical) Genetics data in python

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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 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.

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