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Add a high-level method to assemble single-cell data with AnnData #39

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Add a high-level method to assemble single-cell data with AnnData #39

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@arteymix arteymix commented Oct 3, 2025 •
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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
Improve authentication and path management
4a713d3 
Add an enumeration for all the possible path values.

Allow username to be supplied and password to be prompted with getpass.

Add support for GEMMA_USERNAME, GEMMA_PASSWORD and GEMMA_PASSWORD_CMD
environment variables.
@arteymix
Assemble single-cell data in an AnnData object
7f7d67c
@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
Assemble single-cell data with AnnData #36
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@arteymix arteymix mentioned this pull request Oct 3, 2025
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Assemble single-cell data with AnnData

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