Version 5.1.0

Changes

• Updated interactive SpatialDimPlots to display spatial coordinates
• Updated BuildClusterTree to PseudobulkExpression(..., method = "aggregate") instead of AverageExpression
• Fixed SpatialPlot to properly handle images with shared cells
• Added cluster.name parameter to BuildNicheAssay
• Added VisiumV2 class, inherits SeuratObject::FOV, returned by Load10X_Spatial
• Updated Load10X_Spatial to support loading Visium HD datasets - added bin.size parameter
• Updated Read10X_Coordinates to handle new tissue_coordinates.parquet files
• Added shape parameter to SpatialPlot and wrappers: SpatialFeaturePlot and SpatialDimPlot
• Added image.scale parameter to SpatialPlot and related functions: SpatialFeaturePlot/ISpatialFeaturePlot and SpatialDimPlot/ISpatialDimPlot
• Restored image.name parameter to Read10X_Image
• Added scale parameter to Radius.VisiumV1
• Fixed calculation of spot.radius attribute for VisiumV1 instance returned by Read10X_Image — replace scale.factors$fiducial with scale.factors$spot
• Added Read10X_Coordinates and Read10X_ScaleFactors
• Fixed SpatialPlot to properly handle mutli-assay Seurat instances

Version 5.0.3

Changes

• Fixed PercentAbove to discount null values (#8412)
• Added log parameter to FeatureScatter
• Fixed handling of clip.range for SCTransform when ncells is less than the size of the passed dataset

Version 5.0.2

Changes

• Fixed AverageExpression to handle features vector when layer="scale.data" and return.seurat=TRUE
• Added fc.slot parameter to FindMarkers
• Fixed SCTransform to handle vars.to.regress (#8148) and (#8349)
• Fixed SCTransform to handle fetching residuals (#8185)

Version 5.0.1

Changes

• Fixed SCTransform.StdAssay to pass extra arguments to sctransform::vst(). Fixes #7998
• Fixed PercentageFeatureSet Layer calling #8009
• Fixed cell highlighting #7914
• Updated marker sorting to be by p-value with ties broken by absolute difference in percent expression
• Fixed issue with replicated barcodes in MappingScore #7922
• Improved PseudobulkExpression by adding 'g' to cell names that started with numeric values
• Improved PseudobulkExpression by adding each variable specified in group.by as columns in the object metadata when return.seurat=TRUE
• Fixed DimPlot and FeatureScatter which were breaking when using the split.by argument with a variable that contained NAs

v5.0.0

Added

• Add BridgeCellsRepresentation to construct a dictionary representation for each unimodal dataset.
• Add BuildNicheAssay to construct a new assay where each feature is a cell label. The values represent the sum of a particular cell label neighboring a given cell.
• Add CalcDispersion to calculate the dispersion of features.
• Add CCAIntegration to perform Seurat-CCA Integration.
• Add CountSketch to generate a CountSketch random matrix.
• Add CreateCategoryMatrix to create a one-hot matrix for a given label.
• Add DISP to find variable features based on dispersion.
• Add FastRPCAIntegration as a convenience wrapper function around the following three functions that are often run together when performing integration.
• Add FetchResiduals_reference as a temporary function to get residuals from the reference.
• Add FetchResiduals to call sctransform::get_residuals.
• Add FetchResidualSCTModel to calculate Pearson residuals of features not in the scale.data.
• Add FindBridgeAnchor to find bridge anchors between two unimodal datasets.
• Add FindBridgeIntegrationAnchors to find a set of anchors for integration between unimodal query and the other unimodal reference using a pre-computed BridgeReferenceSet.
• Add FindBridgeTransferAnchors to find a set of anchors for label transfer between unimodal query and the other unimodal reference using a pre-computed BridgeReferenceSet.
• Add GaussianSketch to perform Gaussian sketching.
• Add HarmonyIntegration to perform Harmony integration.
• Add IntegrateLayers to integrate layers in an assay object.
• Add JointPCAIntegration to perform Seurat-Joint PCA Integration.
• Add LeverageScore to compute the leverage scores for a given object.
• Add LoadCurioSeeker to load Curio Seeker data.
• Add MVP to find variable features based on mean.var.plot.
• Add NNtoGraph to convert the Neighbor class to an asymmetrical Graph class.
• Add PrepareBridgeReference to preprocess the multi-omic bridge and unimodal reference datasets into an extended reference.
• Add ProjectCellEmbeddings to project query data onto the reference dimensional reduction.
• Add ProjectData to project high-dimensional single-cell RNA expression data from a full dataset onto the lower-dimensional embedding of the sketch of the dataset.
• Add ProjectDimReduc to project query data to reference dimensional reduction.
• Add ProjectIntegration to integrate embeddings from the integrated sketched.assay.
• Add PseudobulkExpression to normalize the count data present in a given assay.
• Add Read10X_probe_metadata to read the probe metadata from a 10x Genomics probe barcode matrix file in HDF5 format.
• Add RPCAIntegration to perform Seurat-RPCA Integration.
• Add RunGraphLaplacian to run a graph Laplacian dimensionality reduction.
• Add SelectIntegrationFeatures5 to select integration features for v5 assays.
• Add SelectSCTIntegrationFeatures to select SCT integration features.
• Add SketchData to use sketching methods to downsample high-dimensional single-cell RNA expression data for help with scalability for large datasets.
• Add TransferSketchLabels to transfer cell type labels from a sketched dataset to a full dataset based on the similarities in the lower-dimensional space.
• Add UnSketchEmbeddings to transfer embeddings from sketched cells to the full data.
• Add VST to apply a variance stabilizing transformation for selection of variable features.

Changes

• Change FindTransferAnchors so that anchor filtering is not performed by default
• Change merge so that layers will be added to a single Seurat object instead of combining raw count matrices
• Deprecate slot parameter in favor of layers in accessor and set methods

Full Changelog: v4.4.0...v5.0.0

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