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Import additional characteristics from Seurat Disk and AnnData formats #1037

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arteymix opened this issue Feb 16, 2024 · 3 comments · May be fixed by #1020
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Import additional characteristics from Seurat Disk and AnnData formats #1037

arteymix opened this issue Feb 16, 2024 · 3 comments · May be fixed by #1020
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single cell Issues related to single-cell data support

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@arteymix
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arteymix commented Feb 16, 2024

These data formats may include factors that were not reported in the GEO metadata. It would be valuable for curators to have those added to the sample characteristics.

@arteymix arteymix added the single cell Issues related to single-cell data support label Feb 16, 2024
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In the SingleCellDataLoader, I'll add a method to extract characteristics by BioMaterial from the supplied bioassays.

@arteymix arteymix linked a pull request Feb 16, 2024 that will close this issue
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@arteymix arteymix self-assigned this Feb 16, 2024
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I have defined the necessary interface to extract factors and sample characteristics.

I'll work next on extending the GEO loader to import single-cell data.

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This is done for AnnData. We support the full on-disk spec (minus scalar types and akward arrays) and have the ability to detect sample and cell type factors in AnnDataDetector.

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single cell Issues related to single-cell data support
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