Can you name some databases to identify cell types from single-cell data?
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4 months ago
saiteja ▴ 10

I have marker genes. I need to find cell types using these marker genes. Can you suggest some databases to find cell types, the species I'm looking for is Homosepeins?

Also, how to choose one cell type among all the cell types in a cluster. As a result, annotating the cluster with one cell type! Can you answer this please!

rna-seq sequencing tool Assembly single-cell • 259 views
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I am not sure whether there is the one jack-of-all-trades database that will give you every cell annotation that you need.

People commonly annotate clusters of cells using the derived markers based on data from the literature. In most cases a cell type is not new and there are decades of genomics research identifying relevant genes.

There are tools for automated cell type annotation such as SingleR which use a reference/correlation-based approach. You give it a reference dataset, bulk- or scRNA-seq, and then it gives you the most correlated cell type per cluster or even per single-cell. That requires though that you give it a reference that most likely contains the true cell type of origin.

As always it depends, can you comment on which cell types you have, so how the cells have been selected for the library prep?