recommend tools for scRNAseq cell type annotation

Question

[dew]

Dear all,

May I know if there are recommended tools/webs for the cell type annotation?

Say, I have the cell expression matrix, and want to generate a cell type/labels file based on the expression matrix and the prior knowledge of the cell type markers(5-10 genes). The data is from the public data, while only the expression matrix is available to download and no cell type labels file, so trying to generate the cell labels file for downstream analysis.

Thank you very much for all your kind guidance!

Answer 1

[ATpoint]

I like https://github.com/carmonalab/UCell. It calculates a score between 0 and 1 for each marker for every cell based on the ranked expression of these markers and in my hands it worked reasonably robust to get an idea which clusters harbor which celltypes. Including some negative controls make sense, so say you have PBMCs you would include some fibroblast marker signature to see what "background" scores you would get for a celltype not present in your data. The scores you "trust" should then be much higher than that background.

[dew]

Thank you very much! Appreciate!