Run FindAllMarkers on an Azimuth reference

satijalab / azimuth

A Shiny web app for mapping datasets using Seurat v4

https://satijalab.org/azimuth

GNU General Public License v3.0

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Run FindAllMarkers on an Azimuth reference #234

Open maud-p opened 2 months ago

maud-p commented 2 months ago

Dear Azimuth team,

Sorry I have a naive question and can't find a similar issue. I would like to run FindAllMarkers (or similar) on an Azimuth reference to get marker genes for each annotation.

The Azimuth ref contains the $map and $plot Seurat objects. Which one should I use? Any pre-process required? I couldn't make it run so far.

Thank you in advance!