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chanzuckerberg / cellxgene-census

CZ CELLxGENE Discover Census
https://chanzuckerberg.github.io/cellxgene-census/
MIT License
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Bulk download h5ad data with filters [R] #1217

Open myushen opened 3 days ago

myushen commented 3 days ago

Hi, can you please provide guidance on how to download h5ad in bulk with filters of interest in R?

TileDB-SOMA API supports both Python and R, but the documentation only provides Python examples. I tried a similar syntax in R, but it reports that the URI is not a TileDB SOMA object. Am I missing something obvious?

uri = "s3://cellxgene-census-public-us-west-2/cell-census/2023-07-25/soma/"
census <- tiledbsoma::SOMAOpen(uri = uri)

Thanks for your help.

pablo-gar commented 3 days ago

Hi @myushen

Our doc-site has a link to R API & tutorials. You can find more information about R usage there.

You will only be able to download the original h5ads as deposited by contributors via download_source_h5ad using the dataset_id of your data of interest.

If you want to download specific slices of Census after filtering, you can only do so for Seurat or SingleCellExperiment objects.