Discussions

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  Still so confused about assays vs layers in v5.

  ttlyr asked Jul 21, 2025 in Q&A · Unanswered

  

  

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  PrepSCTFindMarkers

  Treshapdesai started Jul 20, 2025 in General

  

  

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  Regress out % mito RNA in snRNAseq OR remove mito genes from VariableFeatures

  tdaf asked Jul 18, 2025 in Q&A · Unanswered

  

  

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  LoadNanostring()/ReadNanostring() Updates

  swbioinf started Aug 26, 2024 in General

  

  

  

  

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  performing FindMarkers on integrated datasets

  kwakuanim started Jul 14, 2025 in General

  

  

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  Workflow for Multi-sample SCTransformed Sketch-based Integration

  TBThien25 asked Jul 11, 2025 in Q&A · Unanswered

  

  

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  Subset Visium-HD data according to spatial location

  grimwoo asked Jul 9, 2025 in Q&A · Unanswered

  

  

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  Question about data access for Parse Biosciences Sketch Integration tutorial

  mbm2224 asked Jun 29, 2023 in Q&A · Unanswered

  

  

  

  

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  RPCA Integration Explained

  sidvmahesh asked Feb 14, 2024 in Q&A · Unanswered

  

  

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  Unexpected UMAP Structure in Pancreatic Visium HD Data Using Seurat v5

  mayurdoke6 asked Mar 25, 2025 in Q&A · Unanswered

  

  

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  No path to doublet removal with BPCells + Seurat — recommendations?

  bug Something isn't working

  keon-arbabi started Jul 3, 2025 in General

  

  

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  How to Analyze Subtypes Within a Rare Cell Population After Integration?

  baiquanCi asked Jul 2, 2025 in Q&A · Unanswered

  

  

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  nCount_SCT varies by batch after SCTransform – normal behavior?

  AndresGithub92 started Jun 30, 2025 in General · Closed

  

  

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  Metafeatures of a seurat object: cannot recompute the exact values of vst.variance.expected and vst.variance.standardized

  gael-millot started Jun 30, 2025 in General

  

  

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  Overlay monocle3 on Seurat integrated object with wnn dimentionality reduction

  oliverabinader started Jun 29, 2025 in General

  

  

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  FindMarkers using paired samples per donor ?

  ptranvan asked Jun 28, 2025 in Q&A · Unanswered

  

  

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  Alternative backend for scatter plot rasterization: {ggrastr} instead of {scattermore}

  pormr started Jun 13, 2025 in Ideas

  

  

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  Data vs Counts-level Variable Features for Spatial Datasets

  CalebYuDot asked Jun 25, 2025 in Q&A · Closed · Answered

  

  

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  Can Seurat use pseudocounts from kallisto (SMART Seq 2) ?

  Achiraa asked Jun 24, 2025 in Q&A · Unanswered

  

  

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  Help Needed: Subsetting Individual Samples from Xenium TMA Data in Seurat

  FenosoaRandrianjatovo started Jun 24, 2025 in General

  

  

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  any movement to macs3 for CallPeaks?

  brianlamere started Jun 23, 2025 in General

  

  

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  choose 'AverageExpression() ' or 'AggregateExpression()' ？

  lilyliushasha asked Jun 22, 2025 in Q&A · Unanswered

  

  

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  Comparison of scRNA datasets via integration analysis

  sketch123456 asked Jun 19, 2025 in Q&A · Unanswered

  

  

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  Strategies for large-scale integration

  johnlee330 asked Jun 19, 2025 in Q&A · Unanswered

  

  

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  FindSpatialVariableFeatures slot options

  kris9393 asked Feb 15, 2025 in Q&A · Unanswered

  

  

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