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cellNexus API refactor #25

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myushen opened this issue Jan 16, 2025 · 0 comments
Closed
10 tasks done

cellNexus API refactor #25

myushen opened this issue Jan 16, 2025 · 0 comments

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@myushen
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myushen commented Jan 16, 2025 •
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Metadata:

  • Rename parameters in metadata.R.
  • Modify get_metadata() to merge metadata from any specified path, indicated by local_metadata and cloud_metadata.
  • Format the Atlas_id column in the metadata to include both atlas id and date, like cellxgene/01_01_2025.

Counts:

  • Remove the atlas_id parameter, as it can be derived from metadata.
  • Restructure the counts hierarchy:
    - cellxgene
    - - 01_01_2025
    - - - counts
    - - - cpm
    - - - pseudobulk
    - - - - counts
    - - - - quantile_normalised
    - - - metacell
    - - - - counts
  • Eliminate the grouping_column parameter.
  • Simplify the get_data_container function.

Test:

  • get_metadata() and get_SCE() are able to query both local and cloud metadata.
  • get_metadata() and get_SCE() are able to query only local metadata.
  • get_metadata() and get_SCE() are able to query only cloud metadata.
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