https://github.com/immunogenomics/starcat_website
https://github.com/immunogenomics/starcat_website
Last synced: 4 months ago
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- Host: GitHub
- URL: https://github.com/immunogenomics/starcat_website
- Owner: immunogenomics
- License: gpl-3.0
- Created: 2024-08-19T18:52:16.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2025-11-07T18:58:08.000Z (7 months ago)
- Last Synced: 2025-11-07T19:14:00.634Z (7 months ago)
- Language: HTML
- Size: 272 KB
- Stars: 0
- Watchers: 10
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE.md
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README
# starCAT Web Application
A privacy-preserving web application for running **starCAT** (star-CellAnnoTator) directly in your browser.
## Overview
starCAT annotates single-cell RNA-seq data with predefined gene expression programs and infers derived discrete annotations such as cell type labels. This web implementation uses **Pyodide** (Python compiled to WebAssembly) to run the complete starCAT algorithm entirely in your browser.
## Key Features
- **Complete Privacy**: All computation happens client-side - your data never leaves your machine
- **No Installation Required**: Run sophisticated bioinformatics analysis directly in your browser
- **Multiple Input Formats**: Takes raw count data in both H5AD (AnnData) and MTX (Matrix Market) file formats
- **Curated Reference Catalogs**: Access to pre-built reference datasets for various tissues and species
- **Zero Infrastructure**: No backend servers or API limits
## Quick Start
1. **Visit the application** (https://immunogenomics.io/starcat)
2. **Select a reference catalog** from the dropdown menu
3. **Choose your file format** (H5AD or MTX)
4. **Upload your data**:
- H5AD: Single `.h5ad` file (up to ~50,000 cells or 700MB)
- MTX: Three files (matrix, features, barcodes)
5. **Click "Run starCAT"** and wait for processing
6. **Download results**: Two TSV files (usage scores and detailed scores) plus interactive visualizations
## Supported File Formats
### H5AD Format
Standard AnnData format for single-cell data stored in HDF5 files.
### CellRanger H5 Format
H5 format output by CellRanger (e.g. filtered_feature_bc_matrix.h5) for users who want to avoid H5Ad
## Reference Catalogs
Pre-built reference catalogs are available for the following:
- Human T cells across tissies and diseases (TCAT.V1)
- Human myeloid cells from gliomas (MYELOID.GLIOMA.V1)
- Human bone marrow derived CD34+ hematapoetic stem cells (BONEMARROW.CD34POS.HSPC.V1)
View the full catalog at the **References** page.
## Local Development
Since this is a static website, you can run it locally with any web server:
```bash
# Using Python 3
python -m http.server 8000
# Using Node.js http-server
npx http-server
# Or simply open starcat/index.html in your browser
```
## Citation
If you use starCAT in your research, please cite:
```
Kotliar, D.*, Curtis, M.*, Agnew, R. et al. Reproducible single-cell annotation of programs underlying T cell subsets, activation states and functions. Nat Methods 22, 1964–1980 (2025). https://doi.org/10.1038/s41592-025-02793-1
```
## Related Resources
- **GitHub** for [starCAT algorithm](https://github.com/immunogenomics/starCAT)
- **Reference Catalogs**: Available on [Zenodo](https://zenodo.org/communities/starcat/records?q=&l=list&p=1&s=10&sort=newest)
- **Documentation**: See [manuscript](https://www.nature.com/articles/s41592-025-02793-1#citeas) for methodology details