https://github.com/bowang-lab/scgpt-spatial
Science Score: 49.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 2 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.2%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bowang-lab
- License: mit
- Language: Jupyter Notebook
- Default Branch: main
- Size: 1.67 MB
Statistics
- Stars: 88
- Watchers: 9
- Forks: 10
- Open Issues: 6
- Releases: 0
Metadata Files
README.md
scGPT-spatial: Continual Pretraining of Single-Cell Foundation Model for Spatial Transcriptomics
🟩 TL,DR Highlights 🟩
✨ Spatial-omic foundation model ✨ ✨ Continual pretraining of scGPT on 30 million cells/spots ✨
✨ Novel MoE (Mixture of Experts) decoders ✨ ✨ Spatially-aware sampling ✨ ✨ Neighborhood-based reconstruction objective ✨
✨ Curation of SpatialHuman30M corpus ✨ ✨ Visium, Visium HD, Xenium, MERFISH ✨
✨ Multi-modal and multi-slide integration ✨ ✨ Cell-type deconvolution ✨ ✨ Missing gene imputation ✨
🟧 Model Weights 🟧
scGPT-spatial V1 weights on figshare.
🟫 SpatialHuman30M 🟫
Pretraining dataset names, slide metadata, and access links are summarized in data source table. Processed data will be available upon publication given permission under license of the original data source.
🟦 Setup and Tutorials 🟦
To start, clone the current repo:
git clone https://github.com/bowang-lab/scGPT-spatial
Special acknowledgement to the scGPT codebase - for environment setup please follow instructions there.
Check out our zero-shot inference tutorial on github! More code coming soon.
🟪 Preprint and Citation 🟪
Check out our preprint! https://www.biorxiv.org/content/10.1101/2025.02.05.636714v1
bibtex
@article{wang2025scgpt,
title={scGPT-spatial: Continual Pretraining of Single-Cell Foundation Model for Spatial Transcriptomics},
author={Wang, Chloe Xueqi and Cui, Haotian and Zhang, Andrew Hanzhuo and Xie, Ronald and Goodarzi, Hani and Wang, Bo},
journal={bioRxiv},
pages={2025--02},
year={2025},
publisher={Cold Spring Harbor Laboratory}
}
Owner
- Name: WangLab @ U of T
- Login: bowang-lab
- Kind: organization
- Location: 190 Elizabeth St, Toronto, ON M5G 2C4 Canada
- Website: https://wanglab.ml
- Repositories: 11
- Profile: https://github.com/bowang-lab
BoWang's Lab at University of Toronto
GitHub Events
Total
- Issues event: 9
- Watch event: 102
- Issue comment event: 11
- Push event: 4
- Public event: 1
- Fork event: 9
Last Year
- Issues event: 9
- Watch event: 102
- Issue comment event: 11
- Push event: 4
- Public event: 1
- Fork event: 9
Committers
Last synced: 12 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| ChloeXWang | 3****g | 11 |
| ChloeXWang | c****q@v****l | 5 |
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 8
- Total pull requests: 0
- Average time to close issues: 36 minutes
- Average time to close pull requests: N/A
- Total issue authors: 8
- Total pull request authors: 0
- Average comments per issue: 0.13
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 8
- Pull requests: 0
- Average time to close issues: 36 minutes
- Average time to close pull requests: N/A
- Issue authors: 8
- Pull request authors: 0
- Average comments per issue: 0.13
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jinxixiang (1)
- qiaoyz23 (1)
- SimonGrouard (1)
- AuthorUnknown404 (1)
- kevinfleisher (1)
- DeevanshuGoyal (1)
- jairaj-mathur (1)
- NBitBuilder (1)