Assigning cell types to cells based on expression of cell surface markers
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12 months ago
Chris Dean ▴ 410

I have a count matrix consisting of cell surface protein abundances output from MissionBio's Tapestri platform using the TotalSeq-D Heme Oncology Cocktail from BioLegend.

I would like to assign cell types to individual cells based on the presence of these surface markers using a reference-based approach, but I am unsure if any exists. I have looked into the celldex package, but these reference databases are derived from bulk rna-seq datasets, which does not seem to be appropriate here.

I am also still quite new to the single-cell domain so it's unclear what the standard is with regards to assigning cell types based on cell surface proteins. In other words, is manual curation - based on canonical markers - or reference-based approaches used more commonly?

Thank you in advance for your input.

tapestri single-cell • 537 views
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maybe this dataset? https://www.nature.com/articles/s41590-021-01059-0

depending on your cell types a reference may not yet exist

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This look promising, thanks so much for sharing ;)!

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