Annotation transfer
Annotated cells
(e.g. published data)
Not-annotated
cells (e.g. your data)
Pros
- Easy to run
- Utilizes existing knowledge
- As good as the alignment
Cons
- Requires pre-annotated data
- Can't be easily tuned
- Isn't aware about cell type relationships
- If it doesn't work there is nothing you can do
Marker-based assignment
*Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling, Nature Methods 2019
Pros
- Intuitive
- Verifiable
- Transferable across datasets
Cons
- Suffers from drop-outs
- Requires detailed annotation
- "Binarizes" expression matrix
- Very laborious