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@arteymix arteymix commented Oct 3, 2025

TODO:

  • concatenate multiple datasets
  • create a multi-index (dataset_id, sample_id, cell_id), the dataset-level can be omitted if a single dataset is requested
  •  include factors, sample characteristics and cell-level characteristics
  • deal with multiple platforms (I think we could use the design element ID for that, or a multi-level index)
  • generalize the concept of download_dir and implement some form of invalidation, I think that the Last-Modified is exposed by the backend and there might even be Cache-Control headers we could leverage there.

Depends on #38 because I needed authentication for the test dataset. The final PR will use a public dataset.

@arteymix arteymix requested a review from oganm October 3, 2025 17:34
@arteymix arteymix linked an issue Oct 3, 2025 that may be closed by this pull request
@arteymix arteymix force-pushed the feature-single-cell-dataset-object branch from 7f7d67c to b93bce7 Compare December 9, 2025 21:53
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Looks like the numerical ID issue is being addressed in scverse/scanpy#3909. We'll have to set the minimum version of scanpy accordingly.

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Assemble single-cell data with AnnData

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