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Our sce-conversion-cheatsheet.md includes a table showing corresponding commands for SCE vs Seurat objects. The Seurat code in here is for Seurat v3 data format, but the default is now v5. We should add an additional column to this table to show v3 and v5 versions, and update additional code as needed.
The text was updated successfully, but these errors were encountered:
the @counts and @data slots are now accessed through $counts and $data; this pattern is available in v3 too, so we can keep that the same.
assay-level metadata is now named @meta.data for all assays, as opposed to the previous @meta.features slot. This is the only difference that I think requires different code depending version: seurat_obj[["RNA"]]@meta.data for v5 and seurat_obj[["RNA"]]@meta.features for v3.
Which is to say I don't think we need a whole new column, just a note for that one entry and a change to the recommendation for the counts and data.
Our
sce-conversion-cheatsheet.md
includes a table showing corresponding commands for SCE vs Seurat objects. The Seurat code in here is for Seurat v3 data format, but the default is now v5. We should add an additional column to this table to show v3 and v5 versions, and update additional code as needed.The text was updated successfully, but these errors were encountered: