Introduction to Vignettes

Welcome to the CASSIA Python 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

1. Basic Annotation - Learn how to use CASSIA to annotate cell clusters using marker files. This covers installation, setup, fast mode, batch analysis, and quality scoring.

2. Clustering and Annotation - A complete workflow starting from raw data using Scanpy. Learn how to cluster single-cell data and annotate it with CASSIA in a seamless pipeline.

3. Extended Analysis - Learn how to use CASSIA's optional agents. This covers uncertainty quantification, annotation boost, RAG, cell type comparison, and subclustering analysis.

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 Python programming
3. Familiarity with single-cell RNA sequencing concepts