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create custom reference dataset #200

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andynkili opened this issue Aug 30, 2021 · 2 comments
Closed

create custom reference dataset #200

andynkili opened this issue Aug 30, 2021 · 2 comments

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@andynkili
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I am trying to infer correctly cell type using SingleR.
I have successfully annotated my Seurat clusters with the HPCA built-in reference (using this link but the results seemed a bit inaccurate.
Now I would like to use custom references. However I cannot find the proper tutorial.
In this link, there is a chapter about custom references but I cannot find how the latter is built.
I have browsed the SingleR issues (closed and open) related to this topic but only found broken url. The closest topic was this one, but it was not clear.
Also I have looked into the SingleR book without finding how to create a reference.
Should I start by creating a SingleR object (as described here) but then how can I use it to infer cell types?
May you point at the right direction/page?

@LTLA
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LTLA commented Aug 31, 2021

Did you read Chapter 3 of the book?

@andynkili
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Thank you.
I found it in the sub-chapter 'Defining custom markers'.

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