Remove contamination across cell clusters

Remove contamination across cell clusters

0

I’ve got an scRNA-seq dataset filtered for immune cells. After applying the Seurat workflow I’ve discovered that some non-immune markers are expressed by cell subsets in almost all the clusters. See heat map:

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I’m fairly certain that those cells are contamination. How would you filter those out based on expression values?

Thanks in advance!


clustering


single-cell

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