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

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

bioinformagician via YouTube Direct link

Data used for demonstration

8 of 17

8 of 17

Data used for demonstration

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

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