https://github.com/JianYang-Lab/gsMap
Integrating GWAS and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.
https://github.com/JianYang-Lab/gsMap
gwas spatial-transcriptomics
Last synced: about 2 months ago
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Integrating GWAS and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.
- Host: GitHub
- URL: https://github.com/JianYang-Lab/gsMap
- Owner: JianYang-Lab
- License: mit
- Created: 2023-12-13T05:49:22.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-02-13T01:52:55.000Z (3 months ago)
- Last Synced: 2025-02-13T02:35:24.078Z (3 months ago)
- Topics: gwas, spatial-transcriptomics
- Language: Python
- Homepage: https://yanglab.westlake.edu.cn/gsmap/home
- Size: 18.3 MB
- Stars: 35
- Watchers: 2
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# gsMap
| | | | |
| ------------- | ---------------------------------------------------------------------------------------------------- | -------------- | -------------------------------------------------------------------------------------------------- |
| __Version__ | [![PyPI version][pypi-badge]][pypi-url] [![Python][python-badge]][python-url] | __Status__ | [![Project Status][status-badge]][status-url] [![Maintenance][maintenance-badge]][maintenance-url] |
| __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] |
| __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] |
| __Downloads__ | [![Downloads][downloads-badge]][downloads-url] | __License__ | [![License: MIT][license-badge]][license-url] [![DOI][doi-badge]][doi-url] |
| __Platform__ | [![Linux][linux-badge]][linux-url] | __Contribute__ | [![Issues][issues-badge]][issues-url] [![PRs Welcome][pr-badge]][pr-url] |
## Introduction
`gsMap` (genetically informed spatial mapping of cells for complex traits)
integrates spatial transcriptomics (ST) data with genome-wide association study (GWAS)
summary statistics to map cells to human complex traits, including diseases,
in a spatially resolved manner.
## Key Features
- __Spatially-aware High-Resolution Trait Mapping__
- __Spatial Region Identification__
- __Putative Causal Genes Identification__
## Installation
Install using pip:
```bash
conda create -n gsMap python>=3.10
conda activate gsMap
pip install gsMap
```
Install from source:
```bash
git clone https://github.com/JianYang-Lab/gsMap
cd gsMap
pip install -e .
```
Verify the installation by running the following command:
```bash
gsmap --help
```
## Usage
Please check out the documentation and tutorials at [gsMap Documentation](https://yanglab.westlake.edu.cn/gsmap/document/software).
## Online Visualization
To visualize the traits-cell association spatial maps,
please refer to [gsMap Visualization](https://yanglab.westlake.edu.cn/gsmap/visualize).
## Citation
Song, L., Chen, W., Hou, J., Guo, M. & Yang, J.
[Spatially resolved mapping of cells associated with human complex traits.](https://doi.org/10.1038/s41586-025-08757-x)
Nature (2025).
Please cite the paper and give us a STAR if you find gsMap useful for your research.
[codecov-badge]: https://codecov.io/gh/JianYang-Lab/gsMap/graph/badge.svg?token=NFZFXZIEUU
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[doi-badge]: https://img.shields.io/badge/DOI-10.1038%2Fs41586--025--08757--x-blue
[doi-url]: https://doi.org/10.1038/s41586-025-08757-x
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[downloads-url]: https://pepy.tech/project/gsMap
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[last-commit-url]: https://github.com/JianYang-Lab/gsMap/commits/main
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[license-url]: https://opensource.org/licenses/MIT
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[python-url]: https://www.python.org
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[ruff-url]: https://github.com/astral-sh/ruff
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