mhkowalski

Hi, Thanks everyone for helpful discussion! I'll reiterate that a gene that is in the counts matrix but is not present in the Seurat object is likely filtered out by...

Hi, Thanks for providing information about this issue. I'm not immediately able to reproduce this. Could you please provide a reproducible example, such as with the data used in this...

Hi, can you please post the full code you are using to run `IntegrateLayers`? We're actually not going to support this in future releases, so I'd recommend not using this...

Thanks for the additional info! Are the results you observe identical with and without the `group.by` parameter? We found that this option was likely not implemented correctly in some cases,...

Hi Andy, Thanks for posting and for using Seurat, and sorry for our delayed response. I'm not what genes you are using as input to `DoHeatmap()`, but you could try...

Hi, We haven't heard back in a while, so I'm going to close this issue. Please feel free to re-open another issue if you continue to have problems, thank you!

Hello, Thanks everyone for your contributions. I'm closing this now as it appears to be resolved, but please open a new issue if you are continuing to have trouble. Thanks!

Hi, Thanks for your question! This a limitation of spatial data, as you mention, because it's not truly single-cell. You could try techniques like RCTD to deconvolve this spot further...

Hi, This is a very old Seurat object so it likely does not work with our current Seurat codebase. Can you please update try running `UpdateSeuratObject()` on your object, or...

Hello, Your code looks reasonable to me, except what is the `disease` variable? Running `SCTransform` on an object with layers split by disease will create a separate model for each...