{"id":33249550,"url":"https://github.com/shz9/magenpy","last_synced_at":"2026-07-01T23:01:49.571Z","repository":{"id":37694680,"uuid":"284605067","full_name":"shz9/magenpy","owner":"shz9","description":"Modeling and Analysis of (Statistical) Genetics data in python","archived":false,"fork":false,"pushed_at":"2026-06-30T17:27:37.000Z","size":2717,"stargazers_count":19,"open_issues_count":7,"forks_count":6,"subscribers_count":1,"default_branch":"master","last_synced_at":"2026-06-30T18:13:05.147Z","etag":null,"topics":["genotype","gwas","ldsc","linkage-disequilibrium","phenotype","prs","simulation"],"latest_commit_sha":null,"homepage":"https://shz9.github.io/magenpy/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/shz9.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.md","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2020-08-03T04:43:34.000Z","updated_at":"2026-06-30T17:26:23.000Z","dependencies_parsed_at":"2025-09-05T16:46:23.800Z","dependency_job_id":null,"html_url":"https://github.com/shz9/magenpy","commit_stats":null,"previous_names":["shz9/gwasimulator"],"tags_count":8,"template":false,"template_full_name":null,"purl":"pkg:github/shz9/magenpy","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/shz9%2Fmagenpy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/shz9%2Fmagenpy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/shz9%2Fmagenpy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/shz9%2Fmagenpy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/shz9","download_url":"https://codeload.github.com/shz9/magenpy/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/shz9%2Fmagenpy/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35025983,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-07-01T02:00:05.325Z","response_time":130,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["genotype","gwas","ldsc","linkage-disequilibrium","phenotype","prs","simulation"],"created_at":"2025-11-16T23:00:23.486Z","updated_at":"2026-07-01T23:01:49.557Z","avatar_url":"https://github.com/shz9.png","language":"Python","funding_links":[],"categories":["Simulation"],"sub_categories":["Mendelian randomization in _cis_"],"readme":"# `magenpy`: *M*odeling and *A*nalysis of (Statistical) *Gen*etics data in *py*thon\n\n[![PyPI pyversions](https://img.shields.io/pypi/pyversions/magenpy.svg)](https://pypi.python.org/pypi/magenpy/)\n[![PyPI version fury.io](https://badge.fury.io/py/magenpy.svg)](https://pypi.python.org/pypi/magenpy/)\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n\n\n[![Linux CI](https://github.com/shz9/magenpy/actions/workflows/ci-linux.yml/badge.svg)](https://github.com/shz9/magenpy/actions/workflows/ci-linux.yml)\n[![MacOS CI](https://github.com/shz9/magenpy/actions/workflows/ci-osx.yml/badge.svg)](https://github.com/shz9/magenpy/actions/workflows/ci-osx.yml)\n[![Windows CI](https://github.com/shz9/magenpy/actions/workflows/ci-windows.yml/badge.svg)](https://github.com/shz9/magenpy/actions/workflows/ci-windows.yml)\n[![Docs Build](https://github.com/shz9/magenpy/actions/workflows/ci-docs.yml/badge.svg)](https://github.com/shz9/magenpy/actions/workflows/ci-docs.yml)\n[![Binary wheels](https://github.com/shz9/magenpy/actions/workflows/wheels.yml/badge.svg)](https://github.com/shz9/magenpy/actions/workflows/wheels.yml)\n\n\n[![Downloads](https://static.pepy.tech/badge/magenpy)](https://pepy.tech/project/magenpy)\n[![Downloads](https://static.pepy.tech/badge/magenpy/month)](https://pepy.tech/project/magenpy)\n\n`magenpy` is a Python package for modeling and analyzing statistical genetics data. \nThe package provides tools for:\n\n* Reading and processing genotype data in `plink` BED format.\n* Efficient LD matrix construction and storage in [Zarr](https://zarr.readthedocs.io/en/stable/index.html) array format.\n* Data structures for harmonizing various GWAS data sources.\n  * Includes parsers for commonly used GWAS summary statistics formats.\n* Simulating polygenic traits (continuous and binary) using complex genetic architectures.\n    * Multi-cohort simulation scenarios (beta)\n    * Simulations incorporating functional annotations in the genetic architecture (beta)\n* Interfaces for performing association testing on simulated and real phenotypes.\n* Preliminary support for processing and integrating genomic annotations with other data sources.\n\n### Helpful links\n\n- [Documentation](https://shz9.github.io/magenpy/)\n- [Citation / BibTeX records](./CITATION.md)\n- [Report issues/bugs](https://github.com/shz9/magenpy/issues)\n\n### AI Usage\n[![AI-DECLARATION: assist](https://img.shields.io/badge/䷼%20AI--DECLARATION-assist-fef9c3?labelColor=fef9c3)](https://ai-declaration.md)\n\nThis project is developed using AI-assisted technologies. Please review our [AI Declaration](AI-DECLARATION.md) for full transparency on automated pipelines.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fshz9%2Fmagenpy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fshz9%2Fmagenpy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fshz9%2Fmagenpy/lists"}