Getting Started

Introduction
Setting Up CASSIA

Basic CASSIA Workflow

Fast Mode
Single Cluster Analysis
Batch Processing
Quality Scoring and Report Generation

Advanced CASSIA Workflow

Introduction to Optional Agents
Uncertainty Quantification (Optional)
Annotation Boost Agent (Optional)
Compare Cell Types (Optional)
Subclustering Analysis (Optional)
Annotation Boost Plus Agent (Optional)
Retrieve Augmented Agent (Optional)

Help

Troubleshooting

Resources

GitHub Repository
Research Paper
Comment Section

CASSIA v1.2.0

Comments

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