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Run KEGG in Seurat object #31

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krigia opened this issue Jul 14, 2023 · 1 comment
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Run KEGG in Seurat object #31

krigia opened this issue Jul 14, 2023 · 1 comment
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@krigia
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krigia commented Jul 14, 2023

@igordot @smped @vreuter @actions-user

Hello msigdbr team,

I am running GSEA analysis in 10X spatial and scRNA-seq data and I would like to use KEGG dataset.
Which function/category should I run?
For Hallmark, I run m_df<- msigdbr(species = "Homo sapiens", category = "H")

but category = "KEGG" does not work. I would greatly appreciate your advice.

Thank you.

@igordot igordot added the question Further information is requested label Jul 14, 2023
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igordot commented Jul 14, 2023

You can check the available collections with msigdbr_collections().

You will see that for KEGG, you want to use msigdbr(species = "Homo sapiens", category = "C2", subcategory = "CP:KEGG").

@igordot igordot closed this as completed Jul 14, 2023
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