Chapter 2 Introduction

In this guide you will learn how to 

– Open a CODEX experiment in CODEX MAV
– Phenotype cells by clustering in Seurat, an R package
– Perform spatial analysis to evaluate spatial proximity

Analysis Overview: 

1. Remove image artifacts and gate on DAPI positive cells (CODEX MAV)
   
2. Identify populations by clustering (R notebook – Seurat)
   
3. Calculate cell neighborhoods (R notebook – Cell neighborhoods)
   
4. Perform spatial analysis (CODEX MAV)