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Automatic Cell-Annotation for Single-Cell RNA-Seq Data Using a Reference Dataset - A SingleR Tutorial
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- 1 Intro
- 2 Overview of cell annotation workflow
- 3 Strategies for automatic cell annotation
- 4 Marker-based annotation approach
- 5 Reference-based annotation approach
- 6 How does SingleR work?
- 7 Study design and goal of the analysis
- 8 Data used for demonstration
- 9 Reading data, filtering and pre-processing in Seurat
- 10 Pointers to choose reference dataset to run SingleR
- 11 Fetching reference data from celldex package
- 12 Run SingleR
- 13 Understanding singleR output
- 14 Visualize singleR labels in a UMAP plot
- 15 Annotation diagnostic 1: Based on scores within cells
- 16 Annotation diagnostic 2: Based on deltas across cells
- 17 Annotation diagnostic 3: Comparing cell type assignments to unsupervised clustering
