Issues

• aggregateNet() fails for single-mode objects and plotly_spatialLRpairPlot() throws "custom_legend" error

  jinworks/SpatialCellChat#17 · Filter by author mapmaker444 opened on Sep 28, 2026
  1

• computeCommunProb does not account for separate samples when calculating spatial distances for multi-ROI / multi-sample data

  jinworks/SpatialCellChat#16 · Filter by author lh12565 opened on Aug 19, 2026

• Failed to install MERINGUE on macOS arm64

  jinworks/SpatialCellChat#15 · Filter by author Ares1314 opened on Jun 30, 2026

• non-conformable matrix dimensions when running computeCommunProb()

  jinworks/SpatialCellChat#14 · Filter by author wykpenguin opened on May 14, 2026
  1

• Performance issue: identifyOverExpressedGenes extremely slow on Xenium data (~36k cells)

  jinworks/SpatialCellChat#13 · Filter by author emily-grantham opened on May 14, 2026
  1

• A few function bodies appear to disagree with their docs / signatures

  jinworks/SpatialCellChat#12 · Filter by author jefferyUstc opened on May 6, 2026

• Error in identifyOverExpressedGenes function

  jinworks/SpatialCellChat#11 · Filter by author liryang opened on Apr 22, 2026

• Multiple sample handing in identifyOverExpressedGenes for spatial data

  jinworks/SpatialCellChat#10 · Filter by author mitharuka opened on Mar 29, 2026

• small count/ weight for Visium hd

  jinworks/SpatialCellChat#8 · Filter by author tetraena123-source opened on Mar 28, 2026

• computeCellDistance memory overload

  jinworks/SpatialCellChat#7 · Filter by author mckoch234 opened on Mar 21, 2026
  3

• Installation fails on R 4.5.3 due to sf / s2 compilation errors

  jinworks/SpatialCellChat#6 · Filter by author asmlgkj opened on Mar 16, 2026

• computeAvgCommunProb_LR_Avg/Sum: format(x, digits=1) >= min.percent performs lexicographic string comparison instead of numeric

  jinworks/SpatialCellChat#5 · Filter by author gettygugu-dot opened on Mar 16, 2026

• computeCommunProb: Matrix::crossprod creates N×N dense intermediate matrix causing OOM on large spatial datasets

  jinworks/SpatialCellChat#4 · Filter by author gettygugu-dot opened on Mar 16, 2026

• computeCellDistance() OOM on Visium HD data: Rfast::Dist() allocates dense N×N matrix (>100K cells)

  jinworks/SpatialCellChat#3 · Filter by author gettygugu-dot opened on Mar 12, 2026

• Compatibility issue with SeuratObject 5.x: slot argument defunct in GetAssayData()

  jinworks/SpatialCellChat#2 · Filter by author RosyGH opened on Mar 3, 2026
  2

• Error in computeCommunProb - missing internal functions?

  jinworks/SpatialCellChat#1 · Filter by author daniannr opened on Mar 2, 2026
  1