CASSIA Documentation
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  • Introduction
  • Setting Up CASSIA
  • Fast Mode
  • Single Cluster Analysis
  • Batch Processing
  • Quality Scoring and Report Generation
  • Uncertainty Quantification (Optional)
  • Annotation Boost (Optional)
  • Compare Cell Types (Optional)
  • Subclustering Analysis (Optional)
  • Annotation Boost Extra (Optional)
  • Troubleshooting
  • Introduction
  • Setting Up CASSIA
  • Fast Mode
  • Single Cluster Analysis
  • Batch Processing
  • Quality Scoring and Report Generation
  • Uncertainty Quantification (Optional)
  • Annotation Boost (Optional)
  • Compare Cell Types (Optional)
  • Subclustering Analysis (Optional)
  • Annotation Boost Extra (Optional)
  • Troubleshooting
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Introduction

CASSIA R Tutorial

Welcome to the CASSIA R tutorial! This guide will walk you through using the CASSIA package in R for cell type annotation using Large Language Models (LLMs).

CASSIA (Collaborative Agent System for Single cell Interpretable Annotation) is a tool designed to enhance cell type annotation by leveraging the power of multi-agent Large Language Models (LLMs).

Let's get started!

Setting Up CASSIA

CASSIA Documentation