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About cell anno in Part2 #6

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mugpeng opened this issue Nov 16, 2022 · 0 comments
Open

About cell anno in Part2 #6

mugpeng opened this issue Nov 16, 2022 · 0 comments

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@mugpeng
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mugpeng commented Nov 16, 2022

Hi,

It's a great work you've done and congratulate.

I notice in the annotation, you used singleR described as:

Part 2: The SingleR package v.1.4.1 (ref. [19](https://www.nature.com/articles/s41588-022-01141-9#ref-CR19)) was used with the Human Primary Cell Atlas database

And I find the reference is not a scRNA dataset, and it's a chip data of human primary cell.
Can you explain why you use chip data instead of scRNA data as reference, because I have never seen people used a non-scRNA data for singleR. And does it make a good sense?
Besides, I can't find the expression data in the reference article, could you serve it for me?
An expression atlas of human primary cells: inference of gene function from coexpression networks | BMC Genomics | Full Text

Thanks a lot, and waiting for you reply.

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