create custom reference dataset

[andynkili]

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]

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

[kusunoky]

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?