Introduction

Overview

Questions

• How to perform differential expression analysis with Seurat?

Objectives

• Gain more familiarity with standard scRNA-seq Quality Control (QC) steps.
• Understand and get comfortable using various integration strategies (harmoy and seuratCCA).
• Understand when and how to use all of the differential expression functions offered by Seurat: FindMarkers(), FindConservedMarkers(), and FindAllMarkers().
• Learn how to use differential expression tools meant for bulk data, like DESeq2, for single-cell ‘pseudobulk’ data and understand why you might choose this approach.
• Learn different ways to visualise both in-built Seurat functions and external packages like pheatmap.

Callout

This tutorial is partially based on existing material from:

• https://satijalab.org/seurat/articles/seurat5_integration
• https://satijalab.org/seurat/articles/de_vignette
• https://hbctraining.github.io/scRNA-seq_online/
• https://bookdown.org/ytliu13207/SingleCellMultiOmicsDataAnalysis/