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Deal with single-cell samples lacking data #1337

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arteymix opened this issue Mar 1, 2025 · 0 comments
Open
3 tasks

Deal with single-cell samples lacking data #1337

arteymix opened this issue Mar 1, 2025 · 0 comments
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single cell Issues related to single-cell data support
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@arteymix
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arteymix commented Mar 1, 2025

Some datasets in GEO only provide data for some of the samples we identify to be single-cell.

It would be unwise to exclude those samples outright as we might have other opportunities to find data elsewhere such as by looking into SRA.

Our data model supports "empty" samples and we use that whenever there are no cells for a given gene. We could use that for every design element. An alternative would be to exclude the sample altogether from the SCD, but that might not play well with the rest of the codebase.

  • add flags to ignore those samples when downloading and loading single-cell data
  • add empty samples to the single cell vectors (or exclude them from the BAD)
  • produce an error if all samples are missing
@arteymix arteymix added the single cell Issues related to single-cell data support label Mar 1, 2025
@arteymix arteymix modified the milestones: 1.32.0, 1.31.13 Mar 1, 2025
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