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Retrieving cluster markers? #108

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shanduur opened this issue May 16, 2022 · 1 comment
Open

Retrieving cluster markers? #108

shanduur opened this issue May 16, 2022 · 1 comment

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@shanduur
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After we run seurat <- RunAzimuth(obj, reference = "./Data/Azimuth/"), is there any way to extract the cluster markers from the clusters itself, or am I only able to use the Annotation Details -> Label/Markers from the website and check intersection of this markers array and genes found in my dataset?

@AustinHartman
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Hi - would you like to find markers for the annotations in the reference or the predicted annotations in the query? Unfortunately, the references do not contain the counts data so it's tricky to identify additional markers not in the tables on the website. If you have particular marker genes in mind I'd encourage you to explore the expression of those genes in the reference viewers (eg: https://azimuth.hubmapconsortium.org/references/human_pbmc/)

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