Metadata-Version: 2.4
Name: gsMap
Version: 1.73.3
Summary: Genetics-informed pathogenic spatial mapping
Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
Requires-Python: >=3.10
Description-Content-Type: text/markdown
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Operating System :: POSIX :: Linux
License-File: LICENSE
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Project-URL: Documentation, https://yanglab.westlake.edu.cn/gsmap/document/software
Project-URL: Home, https://github.com/JianYang-Lab/gsMap
Project-URL: Website, https://yanglab.westlake.edu.cn/gsmap/home
Provides-Extra: doc
Provides-Extra: tests

# 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] |
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| __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__

![Model Architecture](schematic.png)

## Installation

Install using pip:

```bash
conda create -n gsMap python>=3.10
conda activate gsMap
pip install gsMap
```

Install using conda:

```bash
conda create -n gsMap python>=3.10
conda activate gsMap
conda install bioconda::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.

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