CASSIA
Built for biologists, powered by cutting-edge language models.
15-40%
Better than traditional methods
Interpretable
Clear biological reasoning
<2min
Average runtime
1000+
Cell types benchmarked
Validated in real-world single-cell studies and peer-reviewed publications
Quick Start Guide
Get started with CASSIA in just 4 simple steps
1
Configure API
Set up your AI provider key
2
Prepare Data
FindAllMarkers CSV/XLSX file
3
Select Module
Start with Pipeline or Batch
4
Optional Agents
Enhance results with specialized tools
API ConfigurationRequired
Supports OpenRouter, OpenAI, Anthropic, or any custom API. At least one API key is required.
CASSIA Pipeline
🚀 Recommended starting point
- Automated cell type annotation
- Quality scoring and validation
- Annotation merging and grouping
- Boost analysis for challenging clusters
- Interactive HTML reports
CASSIA Batch
🔄 Alternative starting point
- Process multiple clusters in parallel
- Multiple marker ranking methods supported
- Auto-convert gene IDs to gene symbols
- Beautiful interactive HTML reports
- Automatic retry on failures
Optional Agents
🔧 Use after Pipeline/Batch
More advanced agents (Subclustering, Uncertainty Quantification, Symphony Compare) are available in the R and Python packages
Documentation & Resources
Comprehensive guides and examples for CASSIA
Installation & Support
Get CASSIA packages and community support