magenpy

magenpy: Modeling and Analysis of (Statistical) Genetics data in python

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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