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Add tissue and dataset discovery helpers - #155

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stemangiola with Copilot wants to merge 5 commits into
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copilot/add-show-tissues-and-datasets
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stemangiola with Copilot wants to merge 5 commits into
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copilot/add-show-tissues-and-datasets

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Copilot AI commented Aug 28, 2026 •

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CellNexus lacked simple entry points for discovering available tissues and datasets. Add helpers suited to workshops, benchmarks, and routine dataset exploration.

  • Discovery API
    • show_tissues() lists distinct tissue/tissue_groups mappings.
    • show_datasets() lists datasets, optionally filtered by tissue and/or tissue group.
    • Supports custom metadata sources and caching options.
  • Package support
    • Exported both functions and added focused tests/documentation.
show_tissues()

show_datasets(
  tissue = "lung",
  tissue_groups = "respiratory"
)

Copilot AI and others added 4 commits August 28, 2026 02:39
Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
Copilot AI changed the title [WIP] Add show_tissues and show_datasets functions for data exploration Add tissue and dataset discovery helpers Aug 28, 2026
Copilot AI requested a review from stemangiola August 28, 2026 02:41
@myushen

myushen commented Sep 24, 2026

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@stemangiola tissue_groups has been removed from metadata. I wonder whether it is possible to put tissue_groups function mapping as a function in the package? If so, we need to think about how to manage tissues that possibly will be added to the atlas in the future but lack of the mapping.

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add show_tissues and show_datasets(tissue = )

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