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Seurat- SCTransform compatibility? #30
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Hi! Sorry for the late reply, was working on a manuscript deadline. Thanks for pointing this out, I've updated the |
Hi, thank you! I forgot about this but just tried it again today and it works flawlessly now! Just another suggestion: in your Readme, maybe recommend |
Thanks for the suggestion, I just updated to using remotes! Yeah I've noticed devtools does not handle dependencies well too |
Hi @yanwu2014, apologies for the mistake, I double checked and realised it's |
Seems similar to #25.
Typical PBMC 5K data, preprocessed and clustered in Seurat (and native SCTransform).
FindNeighours done, UMAP generated. But
swne.embedding <- RunSWNE(data_transcripts_seurat, k = 20)
Checking my seurat object, it turns out there's no
RNA_snn
, but instead there'sSCT_nn
andSCT_snn
.Would this error be solved by making SWNE look for
object@graphs$SCT_snn
instead? If so, how?The text was updated successfully, but these errors were encountered: