Introduction to Vignettes

Welcome to the CASSIA vignettes section. Here we provide step-by-step tutorials with real data to help you understand the full workflow and capabilities of CASSIA.

Available Vignettes

Our vignettes are organized in increasing complexity:

1. Basic Annotation with Provided Marker Files - Learn how to use CASSIA to annotate cell clusters when you already have marker genes identified.

2. Extended Analysis with Optional Agents - Learn how to use CASSIA's optional agents.

3. Clustering and Annotation Starting from Raw Seurat Object - A complete walkthrough of clustering scRNA-seq data and annotating cell types using CASSIA.

4. Full Workflow Best Practices with Extensive Quality Control - Advanced analysis pipeline with comprehensive quality control steps to ensure robust results. Note: This vignette is still under development and will be expanded in future updates.

Getting Started

To get the most out of these vignettes, make sure you have:

1. CASSIA properly installed (see Setting Up CASSIA)
2. Basic understanding of R programming
3. Familiarity with single-cell RNA sequencing concepts and Seurat

If you have suggestions for additional vignettes or improvements to existing ones, please contribute through our GitHub repository or contact the development team.