Question: How to identify cell types using addModuleScore function?
gravatar for a511512345
6 weeks ago by
China guangxi nanning
a511512345120 wrote:

Hello, there,

I am learning single-cell RNA-seq analysis using Seurat package. I have clustered cells into 12 clusters. Next, I want to identify the cell types of these cell clusters.

I read some paper using addModuleScore function based on the known cell markers. I did not find any example.

however, I do not know how to do identify cell types based on the scores as one cell cluster has several cell type scores. For example, cell cluster one got an average of 0.5 in stem cell score and 0.6 in bronchial epithelial cell score,should the cell cluster one be considered as bronchial epithelial cell?

Need your help very much

Thank you very much

single cell rna-seq • 301 views
ADD COMMENTlink written 6 weeks ago by a511512345120

I have a recent answer on another question that may be helpful for you.

ADD REPLYlink written 6 weeks ago by jared.andrews077.5k

Thank you for this answer. However, I feel very hard to follow the answer as it was not an example.

ADD REPLYlink written 6 weeks ago by a511512345120

There is not a magical answer with your current method - there is no way for us to tell you the appropriate score thresholds to use for your annotations. If you want an automated approach, you can try SingleR, garnet, or any of the various other automated methods.

ADD REPLYlink written 6 weeks ago by jared.andrews077.5k
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