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theislab / zellkonverter

Conversion between scRNA-seq objects
https://theislab.github.io/zellkonverter/
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CITE-Seq Support for Zellkonverter #110

Closed viktorzou closed 6 months ago

viktorzou commented 6 months ago

Hi @lazappi, thx for the great package. I want to use Zellkonverter for conversion of CITESeq data, h5ad -> SCE -> Seurat. I am having trouble finding the Protein Data, where I would expect them (ADT Assay in Seurat object). Is it supported and if yes, where will I find the data or do I have to add the data manually after SC Conversion? best regards Viktor

viktorzou commented 6 months ago

so I found out, that when using Zellkonverter readH5AD() with layers = TRUE, I do get the ADT informatation, but it is not a seperate assay, but appended at the end of the rownames... Is there any possibility to have it seperated as an assay or do I have to seperate it manually?

lazappi commented 6 months ago

This isn't really a {zellkonverter} issue, it's just that AnnData is not designed for multimodal data. Where additional features are stored and how they are converted depends on where the person who created the object decided to store them. In this case it sounds like they were just concatenated to the gene expression matrix.

viktorzou commented 6 months ago

yeah.. it seems to be this way. Thank you. I will manually create the assays, that are needed :)