How to use "SingleR" on the marker genes from `FindAllMarkers` for each cluster?
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11 months ago

Hi,

I tried to use SingleR to identify cell types for clusters. I have the table of results from FindAllMakers of Seurat package.

I know that I can use:

SingleR(GetAssayData(seurat.object, 
        assay = assay, slot = "data"), clusters = Idents(seurat.object),
        ref = hpca.se, labels = hpca.se$label.main)

But is there any way I can utilize the markers for each cluster to define cell types using SingleR ?

Thank you for help.

SingleR seurat scRNAseq scRNA • 2.6k views
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I am also looking for an answer regarding this issue. Any update?

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My problem is similar: I would like to use/compare markers from my dataset and markers from a reference (with labels) to annotate my dataset.

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