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Seurat v4.3.0 compatibility issue #19

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potulabe opened this issue Feb 16, 2023 · 1 comment
Open

Seurat v4.3.0 compatibility issue #19

potulabe opened this issue Feb 16, 2023 · 1 comment

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@potulabe
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potulabe commented Feb 16, 2023 •
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Hi! Thanks a lot for the SignacX package!
I've just encountered a problem, trying to run it with the Seurat v4.3.0, where they had changed column names of a dataframe, returned by the FindMarkers function. So instead of avg_logFC they have avg_log2FC. And because of it the cluster assignment in SignacBoot doesn't work properly.
@potulabe
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potulabe commented Feb 16, 2023 •
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The other issue that I've encountered that the code doesn't work if FindMarkers here in SignacBoot returns 0 or 1 marker genes with avg_log2FC < 0. So I wonder if it is by design that you expect for each cluster to have both positive and negative marker genes.

@akurlovs akurlovs mentioned this issue Mar 6, 2023
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@potulabe