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gsMap\n\n|               |                                                                                                      |                |                                                                                                    |\n| ------------- | ---------------------------------------------------------------------------------------------------- | -------------- | -------------------------------------------------------------------------------------------------- |\n| __Version__   | [![PyPI version][pypi-badge]][pypi-url] [![Python][python-badge]][python-url]                        | __Status__     | [![Project Status][status-badge]][status-url] [![Maintenance][maintenance-badge]][maintenance-url] |\n| __Activity__  | [![GitHub commits][commits-badge]][commits-url] [![Last Commit][last-commit-badge]][last-commit-url] | __Quality__    | [![codecov][codecov-badge]][codecov-url] [![Ruff][ruff-badge]][ruff-url]                           |\n| __CI/CD__     | [![Docs][docs-badge]][docs-url] [![test][test-badge]][test-url]                                      | __Community__  | [![GitHub stars][stars-badge]][stars-url] [![GitHub forks][forks-badge]][forks-url]                |\n| __Downloads__ | [![Downloads][downloads-badge]][downloads-url]                                                       | __License__    | [![License: MIT][license-badge]][license-url] [![DOI][doi-badge]][doi-url]                         |\n| __Platform__  | [![Linux][linux-badge]][linux-url]                                                                   | __Contribute__ | [![Issues][issues-badge]][issues-url] [![PRs Welcome][pr-badge]][pr-url]                           |\n\n## Introduction\n\n`gsMap` (genetically informed spatial mapping of cells for complex traits)\nintegrates spatial transcriptomics (ST) data with genome-wide association study (GWAS)\nsummary statistics to map cells to human complex traits, including diseases,\nin a spatially resolved manner.\n\n## Key Features\n\n- __Spatially-aware High-Resolution Trait Mapping__\n- __Spatial Region Identification__\n- __Putative Causal Genes Identification__\n\n![Model Architecture](schematic.png)\n\n## Installation\n\nInstall using pip:\n\n```bash\nconda create -n gsMap python\u003e=3.10\nconda activate gsMap\npip install gsMap\n```\n\nInstall from source:\n\n```bash\ngit clone https://github.com/JianYang-Lab/gsMap\ncd gsMap\npip install -e .\n```\n\nVerify the installation by running the following command:\n\n```bash\ngsmap --help\n```\n\n## Usage\n\nPlease check out the documentation and tutorials at [gsMap Documentation](https://yanglab.westlake.edu.cn/gsmap/document/software).\n\n## Online Visualization\n\nTo visualize the traits-cell association spatial maps,\nplease refer to [gsMap Visualization](https://yanglab.westlake.edu.cn/gsmap/visualize).\n\n## Citation\n\nSong, L., Chen, W., Hou, J., Guo, M. \u0026 Yang, J.\n[Spatially resolved mapping of cells associated with human complex traits.](https://doi.org/10.1038/s41586-025-08757-x)\nNature (2025).\n\nPlease cite the paper and give us a STAR if you find gsMap useful for your research.\n\n\u003c!-- Badge links --\u003e\n\n[codecov-badge]: https://codecov.io/gh/JianYang-Lab/gsMap/graph/badge.svg?token=NFZFXZIEUU\n[codecov-url]: https://codecov.io/gh/JianYang-Lab/gsMap\n[commits-badge]: https://img.shields.io/github/commit-activity/m/JianYang-Lab/gsMap\n[commits-url]: https://github.com/JianYang-Lab/gsMap/commits/main\n[docs-badge]: https://github.com/JianYang-Lab/gsMap/actions/workflows/docs.yml/badge.svg\n[docs-url]: https://github.com/JianYang-Lab/gsMap/actions/workflows/docs.yml\n[doi-badge]: https://img.shields.io/badge/DOI-10.1038%2Fs41586--025--08757--x-blue\n[doi-url]: https://doi.org/10.1038/s41586-025-08757-x\n[downloads-badge]: https://static.pepy.tech/badge/gsMap\n[downloads-url]: https://pepy.tech/project/gsMap\n[forks-badge]: https://img.shields.io/github/forks/JianYang-Lab/gsMap\n[forks-url]: https://github.com/JianYang-Lab/gsMap/network/members\n[issues-badge]: https://img.shields.io/github/issues/JianYang-Lab/gsMap\n[issues-url]: https://github.com/JianYang-Lab/gsMap/issues\n[last-commit-badge]: https://img.shields.io/github/last-commit/JianYang-Lab/gsMap\n[last-commit-url]: https://github.com/JianYang-Lab/gsMap/commits/main\n[license-badge]: https://img.shields.io/badge/License-MIT-yellow.svg\n[license-url]: https://opensource.org/licenses/MIT\n[linux-badge]: https://img.shields.io/badge/Linux-%E2%9C%93-success\n[linux-url]: https://github.com/JianYang-Lab/gsMap/actions/workflows/test_linux.yml\n[maintenance-badge]: https://img.shields.io/badge/Maintained%3F-yes-green.svg\n[maintenance-url]: https://github.com/JianYang-Lab/gsMap/graphs/commit-activity\n[pr-badge]: https://img.shields.io/badge/PRs-welcome-brightgreen.svg\n[pr-url]: https://github.com/JianYang-Lab/gsMap/pulls\n[pypi-badge]: 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