Automatic Cell-Annotation for Single-Cell RNA-Seq Data Using a Reference Dataset - A SingleR Tutorial

Intro
Overview of cell annotation workflow
Strategies for automatic cell annotation
Marker-based annotation approach
Reference-based annotation approach
How does SingleR work?
Study design and goal of the analysis
Data used for demonstration
Reading data, filtering and pre-processing in Seurat
Pointers to choose reference dataset to run SingleR
Fetching reference data from celldex package
Run SingleR
Understanding singleR output
Visualize singleR labels in a UMAP plot
Annotation diagnostic 1: Based on scores within cells
Annotation diagnostic 2: Based on deltas across cells
Annotation diagnostic 3: Comparing cell type assignments to unsupervised clustering