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mathewchamberlain / SignacX

Signac
GNU General Public License v3.0
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Seurat v4.3.0 compatibility issue #19

Open potulabe opened 1 year ago

potulabe commented 1 year ago

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 commented 1 year ago

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.