gsMap
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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:
conda create -n gsMap python>=3.10
conda activate gsMap
pip install gsMap
Install using conda:
conda create -n gsMap python>=3.10
conda activate gsMap
conda install bioconda::gsmap
Install from source:
git clone https://github.com/JianYang-Lab/gsMap
cd gsMap
pip install -e .
Verify the installation by running the following command:
gsmap --help
🤖 AI-assisted Analysis
gsMap supports AI-assisted workflows that allow users to run spatial GWAS analysis using modern AI coding agents and Vibe coding environments. To add the gsMap MCP server and SKILLs in Claude Code:
cd gsMap/gsmap_vibe
uv pip install -e .
claude mcp add gsmap -- python -m gsmap_mcp
cp -r gsmap_skill ~/.claude/skills/
📘 Usage
Please check out the documentation and tutorials at gsMap Documentation.
🌐 Online Visualization
To visualize the traits-cell association spatial maps, please refer to gsMap Visualization.
📖 Citation
Song, L., Chen, W., Hou, J., Guo, M. & Yang, J. Spatially resolved mapping of cells associated with human complex traits. Nature (2025).
Please cite the paper and give us a STAR if you find gsMap useful for your research.
✨ Research Highlight
gsMap was highlighted in Nature Methods.
gsMap was highlighted in Nature Review Genetics.
1 maintainer
Metadata
1 maintainer
Release files for gsMap 1.73.8
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| gsmap-1.73.8.tar.gz | 71.9 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| gsmap-1.73.8-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 150.1 kB
Release files / gsmap-1.73.8.tar.gz
| Download URL | gsmap-1.73.8.tar.gz |
|---|---|
| Size | 71.9 kB |
| Tags | Source |
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| Size | 78.2 kB |
| Tags | Python 3 |
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| Uploaded via |
twine/7.0.0 CPython/3.13.14
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