Closed dosumis closed 4 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.
obsm
It's missing assay_ontology_term_id. I didn't find yet a mapping for this.
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.