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dputhier / scigenex

This repository stores the scigenex R library.
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Update for Seurat V5 #143

Open Delphine-Potier opened 9 months ago

Delphine-Potier commented 9 months ago

Hi,

I recently switch to Seurat V5 and found out that the current version of scigenex is not compatible with this new version, in which object data access / slots have changed (GetAssayData() is deprecated and "slots" are "layers" ).

It at least needs an update of the function get_data_for_scigenex() called by select_genes() For "data" and "count" which_slot options

data <- SeuratObject::GetAssayData(data, slot = which_slot) to be replace by

  data <- SeuratObject::LayerData(Seurat, layer = which_slot, assay = "RNA")

And probably also for "sct" to change data@assays$SCT@data to include "@layer" I didn't go further yet, but there may be more updates to perform.

Thanks for this nice tool!

dputhier commented 9 months ago

Hi Delphine, We will have a look ASAP. Best