Marcel Schilling
Marcel Schilling
I did not. Regarding the exact modification, like I said, I passed `layer = counts` instead of relying on the default value.
I actually hit this again myself. At this point I just regret using Seurat after it clearly got out of hand maintainance-wise and will likely switch to scanpy for future...
@longmanz: Thank you for the reply. I'll look into it as soon as I can an report back. If this problem is know and the fix is just a few...
@longmanz: After a first quick check your workaround seems to be working! 🎉 Thank you! ❤️ Any chance to get this into a PR at least? 😉
Here is the generalized workaround I ended up using (I have objects with > 1 SCT assays): ```r require(magrittr) require(SeuratObject) sobj
@gabsax: Have you tried @p-gueguen's suggestion of setting `method = "wkde"`? It works for me.
@gabsax: > ...but the result it's not accurate. Could you elaborate?
Interesting example. I guess it's the negative values that create the difference. So there are lots of cells expressing the feature but those are balanced out by a lot of...
@Juke34: I hit the same issue with AGAT 1.3.3. I'll try reproducing with the latest version and will report back.
We are still getting an error when trying to build a custom Cell Ranger index based on the AGAT-merged GTF, even when using v.1.4.0. I'll try to provide more details...