Spike on reading atlas data from CELLxGENE census API - Githubissues

DataBiosphere / data-portal

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Spike on reading atlas data from CELLxGENE census API #2376

Closed NoopDog closed 1 month ago

NoopDog commented 4 months ago

Need

Review the CELLxGENE census API to review the attributes that can be extracted/summarized for presentation on the Atlas Explorer.

In a Jupyter notebook

[ ] Create a query to read the HCA Lung V1 Atlas data from the CELLxGENE soma API. Review if this query can be made sharable on the portal.
[ ] Extract the Cell Types standard category cell types, count of individual cell types.
[ ] Extract the ann_finest_level (are the nonstandard categories available in census?)
[ ] What embeddings are available? e.g. Is it possible to reconstruct the umap for the atlas with cell type labels?

NoopDog commented 1 month ago

Complete