Automated Cell Type
Annotation Platform
Transform your single-cell RNA-seq analysis with AI-powered precision. Upload marker data, configure your analysis, and receive comprehensive cell type annotations with detailed reports.Built for biologists, powered by cutting-edge language models.
Validated in real-world single-cell studies and peer-reviewed publications
Quick Start Guide
Get started with CASSIA in just 4 simple steps
Configure API
Set up your AI provider key
Prepare Data
FindAllMarkers CSV/XLSX file
Select Module
Start with Pipeline or Batch
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.
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.
- Automated cell type annotation
- Quality scoring and validation
- Annotation merging and grouping
- Boost analysis for challenging clusters
- Interactive HTML reports
- Process multiple clusters in parallel
- Configurable worker count
- Automatic retry on failures
- Comprehensive CSV reports
- Best for large datasets