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Update sce conversion cheatsheet to use Seurat v5 #831

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sjspielman opened this issue Dec 18, 2024 · 2 comments
Open

Update sce conversion cheatsheet to use Seurat v5 #831

sjspielman opened this issue Dec 18, 2024 · 2 comments

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@sjspielman
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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.

@sjspielman
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Noting this Seurat command list for v5: https://satijalab.org/seurat/articles/seurat5_essential_commands

@jashapiro
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jashapiro commented Dec 18, 2024

I think that the main differences are:

  • 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.

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