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Filter which subsets are retained when generating pseudo-bulks #1279

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arteymix opened this issue Oct 31, 2024 · 1 comment
Open

Filter which subsets are retained when generating pseudo-bulks #1279

arteymix opened this issue Oct 31, 2024 · 1 comment
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@ppavlidis @arteymix @rachadele
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enhancement Enhance the code or user experience single cell Issues related to single-cell data support

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arteymix commented Oct 31, 2024 •
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We need criterias to retain a pseudo-bulks.

We have access to the following metrics:

  • number of expressed genes
  • number of cells
  • number of nnz

More can be computed if needed.

For now, I'll implement a nnz > 0 strategy.
@arteymix arteymix added enhancement Enhance the code or user experience single cell Issues related to single-cell data support labels Oct 31, 2024
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arteymix commented Dec 4, 2024

This is related to #1287 as cell filtering will affect the sparsity of the pseudo-bulk.

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enhancement Enhance the code or user experience single cell Issues related to single-cell data support
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@ppavlidis @arteymix @rachadele