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joeb-liver / Single_Cell_Liver_Atlas

R code for metaanalysis of single cell liver data
GNU General Public License v3.0
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how to map clusters #3

Open star9926 opened 2 years ago

star9926 commented 2 years ago

Hello, I really appreciate your efforts and information for the single cell sequencing from human liver, that does inspire me a lot, while I have a question about how to map the real cell type to the final cluster, in your project, there was only a new vector named new.cluster.ids, which directly named the final clusters. Is thre any explanation for annotation with cell biomarkers, manually or automated?

Thanks a lot, Na

joeb-liver commented 2 years ago

Hi Na,

Thanks for the question! We are liver biologists in my lab so we annotated the clusters manually using known markers in the field. I think new tools like Azimuth might help with annotation in the future, but there still isn't a liver reference set yet. You can reach out to me at my email @.***) if you have more questions or want to know particular markers for particular cell types.

-Joe

From: starshine @.> Sent: Monday, June 27, 2022 12:49 PM To: joeb-liver/Single_Cell_Liver_Atlas @.> Cc: Subscribed @.***> Subject: [joeb-liver/Single_Cell_Liver_Atlas] how to map clusters (Issue #3)

Hello, I really appreciate your efforts and information for the single cell sequencing from human liver, that does inspire me a lot, while I have a question about how to map the real cell type to the final cluster, in your project, there was only a new vector named new.cluster.ids, which directly named the final clusters. Is thre any explanation for annotation with cell biomarkers, manually or automated?

Thanks a lot, Na

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star9926 commented 2 years ago

Dear Joe,

Exactly! Thanks a lot for your reply, I will try to manually mapped to the clusters from human liver data. I knew [Tabula Muris Consortium] developed TabulaMurisData which included various tissue for mice, and could be used for data from mouse with specialized tissues, like liver. They also have similar data for human, https://pubmed.ncbi.nlm.nih.gov/35549404/ , but still no open data available in R. Hopeful soon for automatically usage. P.S. I could not see your email, it could be great if you send me the annotiation for liver cell in your research, I want to use it for reference. my emails is nanaliu0206@icloud.com. Thanks again!

Best regards, Na