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 Configuration RequiredRequired
Set up your AI provider API key to start analyzing your data. This is required for all analysis features.
OpenRouter (Recommended)
OpenAI GPT Models
Anthropic Claude
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Why do I need an API key?
CASSIA uses advanced AI language models to analyze your cell marker data and provide intelligent annotations. You need an API key from OpenRouter, OpenAI, or Anthropic to access these models. Your key is stored securely in your browser and never shared with our servers.
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
- Configurable worker count
- Automatic retry on failures
- Comprehensive CSV reports
- Best for large datasets
Optional Agents
🔧 Use after Pipeline/Batch
Documentation & Resources
Comprehensive guides and examples for CASSIA
Installation & Support
Get CASSIA packages and community support