NICHES with Seurat v5 layers

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I just have a tip to share in case anyone out there runs into the same problem that I was having.

When using Seurat v5 (technically Seurat v4.9.9.9040), due to the new "layer" structure of the Seurat object, the scc.merge step doesn't combine the counts layers. Instead of just having one merged "counts", I had "counts.1" and "counts.2" in my scc.merge. This didn't allow me to (1) continue on with the NICHES workflow, and (2) DimPlot my second condition and would instead show something like this in the console:

To resolve this, just after running scc.merge <- merge(temp.list[[1]],temp.list[[2]]), I would run "scc.merge <- JoinLayers(scc.merge)". This should join the two "counts.1" and "counts.2" into one single "counts" layer, and should allow to proceed with the NICHES workflow.

Alternatively, downgrading Seurat to v4 avoids this issue in the first place.