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Documenting pseudobulk DE analysis#10417

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mukamel-lab wants to merge 5 commits into
satijalab:mainfrom
mukamel-lab:docs/de_pseudobulk
Open

Documenting pseudobulk DE analysis#10417
mukamel-lab wants to merge 5 commits into
satijalab:mainfrom
mukamel-lab:docs/de_pseudobulk

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Summary

Type of change

  • Bug fix (non-breaking change fixing an issue)
  • New feature (non-breaking change adding functionality)
  • Breaking change (existing functionality changed or removed)
  • [ X] Documentation update
  • Other (please explain below)

Motivation

Clarifies the documentation and vignette relating to the use of FindMarkers() for differential expression analysis, highlighting the issues with using pseudoreplicates (i.e. single cells as the unit of analysis) for DE analysis of samples from different conditions.

Tests & examples

# Example code here

Related issues

Closes #9199

Checklist

  • [ x] Branch is named appropriately (feat/*, fix/*, docs/*)
  • [ x] Code follows Seurat style guidelines
  • [ x] Documentation and comments have been updated
  • [ x] devtools::document() has been run
  • [ x] devtools::check() passes with no errors or warnings
  • Test case demonstrating new functionality is included
  • [ x] Maintainers are allowed to edit this PR

@anashen
anashen force-pushed the docs/de_pseudobulk branch from 74e8491 to 451b345 Compare June 26, 2026 13:41
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Clarify documentation of DEG/DAR methods

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