Issues

• RunUMAP/RunPCA reproducibility: embeddings depend on the ambient RNG stream, thread counts, and unpinned uwot defaults

  satijalab/seurat#10502 · Filter by author BenjaminDEMAILLE opened on Sep 10, 2026

• as.Seurat Fails For Scrapper-generated Dataset

  bug
  satijalab/seurat#10499 · Filter by author DarioS opened on Sep 2, 2026

• Matrices past the dgCMatrix 2^31 limit, cut into reviewable pieces

  satijalab/seurat#10498 · Filter by author BenjaminDEMAILLE opened on Sep 1, 2026
  5

• Index of my open PRs: 53 grouped into 10, all draft

  satijalab/seurat#10486 · Filter by author BenjaminDEMAILLE opened on Sep 1, 2026
  5

• SketchData and ComBat-seq compatibility

  satijalab/seurat#10446 · Filter by author gboscagli opened on Aug 21, 2026

• BUG: MapQuery gives aberrant results if reference is subset after RunUMAP

  bug
  satijalab/seurat#10445 · Filter by author Alexis-Varin opened on Aug 20, 2026
  1

• BUG: FindClusters function always fall back to Louvain clustering even if I tried both leidenbase and igraph methods

  bug
  satijalab/seurat#10436 · Filter by author alexwu66666 opened on Aug 7, 2026
  5

• Feature Request: Add parameter for compact segmentation on LoadXenium() function to improve Xenium scalability

  enhancement
  satijalab/seurat#10431 · Filter by author diego-iac opened on Jul 29, 2026
  

• Documentation: <visium data of rctd>

  documentation
  satijalab/seurat#10428 · Filter by author asmlgkj opened on Jul 21, 2026

• Does FindClusters order/renumber clusters by size (largest cluster first)

  bug
  satijalab/seurat#10425 · Filter by author asmlgkj opened on Jul 14, 2026
  2

• BUG: Setting multiple cores in future causes IntegrateLayers to go into an infinite loop

  bug
  satijalab/seurat#10420 · Filter by author chlige opened on Jun 29, 2026
  3

• Feature Request: Change the default value of margin parameter to 2 in NormalizeData() for CLR normalization

  enhancement
  satijalab/seurat#10416 · Filter by author javier-marchena-hurtado opened on Jun 25, 2026

• RNA assay has no layers after running harmony integration followed by rejoining layers

  satijalab/seurat#10415 · Filter by author gabrielleper opened on Jun 25, 2026
  3

• BUG: Potential issue in parallel memory usage

  bug
  satijalab/seurat#10406 · Filter by author rbutleriii opened on Jun 11, 2026
  8

• FindMarkers returns an empty data frame with "No features pass min.pct threshold" even though min.pct = 0

  satijalab/seurat#10394 · Filter by author Mint-hx opened on May 20, 2026
  8

• Feature Request: Support ggmlR as an optional backend for universal GPU acceleration

  enhancement
  satijalab/seurat#10381 · Filter by author Zabis13 opened on Apr 30, 2026

• BUG: FeaturePlot generates empty plot when plotting and rasterizing multiple features (raster, order, combine = T)

  bug
  satijalab/seurat#10346 · Filter by author YoukaiFromAccounting opened on Mar 25, 2026
  1

• What have residual features argument in SCTransform done?

  satijalab/seurat#10297 · Filter by author shihsama opened on Feb 5, 2026
  1

• TransferData error :Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds

  satijalab/seurat#10279 · Filter by author xiangyupan opened on Jan 17, 2026
  1

• BUG: seurat-wrappers::alra.R

  bug
  satijalab/seurat#10252 · Filter by author turkeyri opened on Dec 17, 2025
  1

• FindIntegrationAnchors Hangs When Run in Parallel

  satijalab/seurat#10238 · Filter by author mfurla opened on Dec 11, 2025
  2

• Regression: ReadXenium does no longer apply transcript QV filtering

  bug
  satijalab/seurat#10155 · Filter by author ppm1337 opened on Oct 23, 2025
  2

• Not a BUG: SCTransform suddenly runs into future errors

  bug
  satijalab/seurat#10130 · Filter by author BioinfSina opened on Oct 13, 2025
  2

• BUG: Cell order in sparse count matrix affects ScaleData() results and downstream PCA/UMAP

  bug
  satijalab/seurat#10033 · Filter by author JLiLab opened on Aug 4, 2025
  5

• Proposal: Add RunscDblFinder() and RunDoubletFinder() with unified RunDoubletDetection() wrapper

  satijalab/seurat#10022 · Filter by author BenjaminDEMAILLE opened on Jul 28, 2025
  1