Version 4.4.0

Added

• Added parallelization support with speed improvements for PrepSCTFindMarkers
• Fix bug in LoadNanostring(#7566)

Changes

• Fix bug in as.Seurat.SingleCellExperiment() (#6692)
• Support for Visium probe information introduced in Spaceranger 2.1 (#7141)
• Add LoadCurioSeeker to load sequencing-based spatial datasets generated using the Curio Seeker
• Fix fold change calculation for assays (#7095)
• Fix pt.size bug when rasterization is set to true (#7379)
• Fix FoldChange and FindMarkers to support all normalization approaches (#7115,#7110,#7095,#6976,#6654,#6701,#6773, #7107)
• Fix for handling newer ParseBio formats in ReadParseBio (#7565)
• Fix for handling rasterization by default (#7842)
• Fix sce object conversion by @timoast in #6771
• Fix(Xenium): load renamed feature by @jsicherman in #6986
• keep.scale for SpatialPlot/SpatialFeaturePlot by @samuel-marsh in #6905
• spaceranger 2.1 update by @stephenwilliams22 in #7141
• update ReadParseBio to be compatible with latest split-pipe v1.1.0 by @epapalexi in #7565
• Correct lost gene expression column when loading NanoString CosMx data by @mtgregory in #7566

New Contributors

• @jsicherman made their first contribution in #6986
• @mtgregory made their first contribution in #7566

Full Changelog: v4.3.0...v4.4.0

Version 4.3.0

Added

• Add support for imaging-based spatial datasets

Changes

• Fix bug in FindMarkers() when run post Integration/Transfer (#6856)

Version 4.2.0

Changes

• Fix legend color in DoHeatmap() (#5783)
• Fix bug in ScaleData() when regressing out one gene (#5970)
• Fix name pulling in PlotPerturbScore() (#6081)
• Support spaceranger 2.0 (#6208)
• Fix bug in SpatialDimPlot() when using group.by (#6179)
• Add add.noise parameter in VlnPlot()
  (#5756)
• Fix uwot model backwards compatibility (#6345)
• Allow pseudocount.use in differential expression functions to be set at the Assay level

Version 4.1.1

Changes

• Fix giveCsparse related warnings in Read10X_h5
• Fix ident labeling for SpatialPlot (#5774)
• Fix ReadMtx on Windows (#5687)
• Fix VlnPlot to switch on rasterization only when required (#5846)
• Fix ncol behavior in SpatialPlot (#5774)
• Set jitter to FALSE in FeatureScatter (#5876)
• Update Cells methods to new signature (x, ...)
• Replace use of default.stringsAsFactors() with getOption("stringsAsFactors")

Version 4.1.0

Changes

• Update ReadParseBio to support split-pipe 0.9.6p (#5446)
• Fixes for MAST differential expression (#5441)
• Fix scaling options when using split.by in FeaturePlot() (#5243)

Additions

• Add raster.dpi parameter to DimPlot/FeaturePlot to optionally rasterize individual points (#5392)
• Add support for sctransform v2, differential expression on with SCT

Version 4.0.6

Changes

• Add raster parameter to VlnPlot to optionally rasterize individual points (#5076)
• Add min.cells.group parameter to FindConservedMarkers (#5079)
• Set do.center to FALSE for lsiproject in FindTransferAnchors
• Fix error message in ReadMtx() (#5158)
• Add label.color parameter to FeaturePlot (#5314)
• Fix issues in ProjectUMAP (#5257, #5104, #5373)

Additions

• Implement supervised LSI

Version 4.0.5

Changes

• Update documentation for to.upper parameter in Load10X_Spatial() (#4576)
• Update concept tags for RunSPCA() (#4978)
• Conditionally run tests/packages that use suggested packages (#5160)

Version 4.0.4

Changes

• Warn and continue rather than erroring if not all features are available in FindSpatiallyVariableFeatures() (#4611)
• Bug fix for SCT-based integration in selecting proper reference model (#4355)
• Bug fix for reading from absolute paths in ReadMtx (#4723)
• Bug fix in SingleCellExperiment conversion (#4633)
• Bug fix in FindVariableFeatures() when using selection.method = "mvp" and binning.method = "equal_frequency" (#4712)
• Bug fix in DoHeatmap() to remove random characters from plot legend(#4660)
• Fix cell renaming in RunCCA()
• Fix issue in SingleCellExperiment conversion where the mainExp would not be set properly
• Fix for default dispersion info displayed in VariableFeaturePlot()

Additions

• Add reduction parameter to BuildClusterTree() (#4598)
• Add DensMAP option to RunUMAP() (#4630)
• Add image parameter to Load10X_Spatial() and image.name parameter to Read10X_Image() (#4641)
• Add ReadSTARsolo() function to read output from STARsolo
• Add densify parameter to FindMarkers()
• Add ReadParsebio() function to read output from Parse Biosciences
• Add the image.alpha parameter to SpatialDimPlot() and SpatialFeaturePlot()

Version 4.0.3

Changes

• Fix issues with as.SingleCellExperiment.Seurat() for the latest verion of SingleCellExperiment (#4532)
• Ensure proper reference.reduction is used in MapQuery()
• Fix to UpdateSymbolList(), no longer searches aliases and exposes the search.types parameter in GeneSymbolThesarus() (#4545)
• Transfer scale.data slot as well when converting with as.SingleCellExperiment.Seurat()
• Enable alpha parameter for SpatialDimPlot()
• Fix as.SingleCellExperiment.Seurat() conversion for atypical reducedDim components

Additions

• Add jitter parameter to FeatureScatter()

Version 4.0.2

Changes

• Preserve feature metadata when converting from SingleCellExperiment to SeuratObject class
  (#4205)
• Preserve multiple assays when converting from SingleCellExperiment to SeuratObject class
  (#3764)
• Fix passing of score.thresh parameter in ScoreJackStraw() (#4268)
• Fix FC calculation in FindMarkers() non-log transformed data.
• Add umap-learn version >= 0.5.0 compatibility for RunUMAP()
• Fix DotPlot to use log1p when scale=False
  (#4298)
• Fix split and shuffled DimPlot
• Disallow NULL or another length 0 vector for ident.1 in FindMarkers()
• Fix range shift when labeling clusters on a GeomSpatial plot
• Fix SpatialPlot distortion for non-square images.
• Fix future-related warnings in FindIntegrationAnchors()
• Fix fc.name parameter in FindMarkers() (#4474)
• Deprecate group.by parameter in PlotPerturbScore() in favor of mixscape.class.

Additions

• New AddAzimuthScores() and AddAzimuthResults() functions
• Add shuffle parameter to FeatureScatter() (#4280)
• Add lsiproject and rpca options for FindTransferAnchors()
• Add rlsi option for FindIntegrationAnchors()