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EBISPOT / scxa_2_cxg

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Write scxa->cxg h5ad converter - obs only #1

Closed dosumis closed 4 months ago

dosumis commented 5 months ago

CxG Standard - latest approved version: https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/4.0.0/schema.md

Example h5ad file on scxa FTP: https://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/E-CURD-2/

Attempt at mapping obs between schemas here: https://github.com/VirtualFlyBrain/scxa-to-h5ad/issues/1#issue-1881521372

It is also worth checking vars for compliance (making sure gene name. ID and type are stored in a schema compliant way.

Finally - obsm stored embeddings. Ideally this would be compliant too.

anitacaron commented 4 months ago

It's missing assay_ontology_term_id. I didn't find yet a mapping for this.