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Version 5.5.0

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@anashen anashen released this 22 Apr 14:06
v5.5.0
999195c
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Learn about vigilant mode.

Changes

Additions

  • Added support for vars.to.regress and latent.data in ScaleData.IterableMatrix (BPCells) (#10300)
  • Added warning to SCTransform to notify that do.correct.umi is hard set to F when a reference SCT model is specified (#10329, #10366)
  • Added warning to FindMarkers/FindAllMarkers when running on an IterableMatrix (BPCells) with column-major storage order (#10365)
  • Added plot_type parameter to ElbowPlot to switch between default (PCs x standard deviation) and two new options:
    • PCs x % variance explained (#8929)
    • PCs x cumulative % variance explained (#10369)
  • Added legend.position parameter DimHeatmap to allow repositioning of legend when combine = T (#9813)
  • Added "selected cells" indicator in InteractiveSpatialPlot (#10254)
  • Added stroke.alpha parameter to SpatialPlot to be able to control transparency for fill and stroke separately (#10345)
  • Added support for unnamed cols vectors in SpatialPlot (#10298)
  • Added assay parameter to FeaturePlot to specify assay to pull features from (#10349)

Fixes

  • Fixed issue with UMAP version parsing in RunUMAP (#10246)
  • Updated HTODemux to handle HTO assays containing a subset of cells (#10362)
  • Updated Rcpp error handling (#10317, #10353)
  • Fixed issue with NaN values being propagated in PrepSCTFindMarkers (#10361)
  • Fixed umi.assay labeling for model list in SCTransform to match the assay specified (#10330)
  • Fixed factor-level ordering for metadata columns resulting from FindClusters (#10253)
  • Fixed error in FindSpatiallyVariableFeatures from use of slot in function cascade (#10285)
  • Fixed classification of gRNA with less than 5 cells in RunMixscape for proper label as "NP" (#10299)
  • Fixed issue with checking object scope in as.Seurat.SingleCellExperiment (#10339)
  • Fixed SketchData to pass the provided argument for verbose to LeverageScore (#10145)
  • Fixed FindConservedMarkers to pass the provided argument for min.cells.group to FindMarkers (#8910)
  • Updated IntegrateEmbeddings to respect dims.to.integrate when reference is specified (#10172)
  • Fixed list structure of neighbors in FindNeighbors when SNN is not computed (#10364)
  • Updated DimHeatmap to add PC labels as individual titles (#9813)
  • Updated layer-building logic in Single/MultiExIPlot for ggplot2 v4+ compatibility (#10333)
  • Fixed order = T in rasterized Dim/FeaturePlots via ggrastr-based rasterization (#10307, #10344)
  • Updated SpatialPlot coordinate system check when plotting VisiumV1 images (#10267)
  • Updated SpatialPlot for Visium data to speed up plot construction (#10345)
  • Fixed interactive functionality of LinkedDim/LinkedFeaturePlot and interactive mode in SpatialPlot (#10368)
  • Updated coordinate systems used for plot display in InteractiveSpatialPlot (#10254)
  • Fixed coordinate ranges when spatial plots are generated with crop = F (#10278, #10284)
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