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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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create custom reference dataset #148

Closed andynkili closed 1 year ago

andynkili commented 2 years ago

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?

dviraran commented 2 years ago

Please, issues go in this repository: https://github.com/LTLA/SingleR

kusunoky commented 1 year ago

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?

Hi I'm having the same issue. @andynkili did you come up with any solution? could you please give me some advice?