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LungCellAtlas / HLCA

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HLCA-core Seurat Object normalised counts #9

Closed carissaynchen closed 1 year ago

carissaynchen commented 1 year ago

Hello,

I downloaded the seurat object from cellxgene but I can't find the normalised counts in scale.data nor assays slot, and I can only find the raw counts. Is it only available in the adata object?

LisaSikkema commented 1 year ago

Hi @carissaynchen ,

I haven't worked with the Seurat Object myself (it was automatically generated by cellxgene), but would this page be of help? https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/3.0.0/seurat_encoding.md

If not, I can check with the cellxgene people

carissaynchen commented 1 year ago

Ah, it's there, thank you!