Version 5.4.0

Changes

Additions

• Added support for 10x Space Ranger 4.0 outputs (Visium data with segmentations)
  • Updated data loading functions Load10X_Spatial, Read10X_Image
  • Updated GetTissueCoordinates.VisiumV2
  • Updated spatial visualization functions SpatialPlot, SingleSpatialPlot, SpatialDimPlot, SpatialFeaturePlot
  • Added helper functions Read10X_Segmentations, Read10X_HD_GeoJson, Format10X_GeoJson_CellID
• Added function InteractiveSpatialPlot to allow users to interactively lasso-select cells from a spatial Seurat object (Visium, SlideSeq, or Vizgen data)

Fixes

• Updated loading & visualization functions (see above for list) for Visium objects -- see #10125 for details
  • For binned Visium data, x now correctly corresponds to imagecol from tissue positions; y now correctly corresponds to imagerow from tissue positions; these are now consistent with 10X's coordinate system (with the origin being the top left).
• Reverted #10062 in favor of fetching both grouping variables and dimensionality reduction embeddings with FetchData as previously; added warning to alert users when column names of metadata and dimensionality reduction embeddings conflict
• Added color retrieval logic in LabelClusters for consistent cluster label coloring (#10198)

Version 5.3.1

Changes

Additions

• Added option to use cluster_leiden from igraph when running Leiden clustering (#9931)
• Added option to use umap2 from uwot when running UMAP (#9918)
• Added option to use approx_pow parameter from uwot when running UMAP (#9449)
• Updated LoadXenium to add support for Xenium protein data (#10024)
• Added option to specify stroke size in FeaturePlot (#10053)
• Added label.size.cutoff parameter to DimPlot to allow users to label only clusters above a certain size (#10092)

Fixes

• Fixed deprecated calls to Seurat functions GetAssayData and PackageCheck (#9924), (#10102)
• Fixed errors in RunAzimuth relating to FindTransferAnchors (#9924)
• Fixed errors in LeverageScore relating to handling of (variable) features (#9924)
• Updated PseudobulkExpression to acccount for the case that a category passed to group.by has only one value (#10092)
• Updated VlnPlot to use assay passed to the function if specified (#10092)
• Updated FeatureScatter to allow gene names with parentheses to be plotted (#10092)
• Updated SingleRasterMap to store object metadata correctly (#10092)
• Updated FindClusters to order cluster factor levels correctly when assigning a custom cluster name (#10092)
• Updated FindConservedMarkers to remove NA values (#9917)
• Updated visualization functions to avoid ggplot2 guides, aes_string, and facet_grid deprecation warnings (#9409, #10116)
• Fixed DimPlot bug where metadata columns named 'PC_1', 'UMAP_1' etc override reduction embeddings (#10062)

Version 5.3.0

Bug releases and performance improvements, including:

• Refactoring and speed-up of sctransform
• Refactroring and speed-up of leverage score calcluation
• Fixes to variable feature selection, module score calculation, PseudobulkExpression, and other bugs that could cause errors in edge cases
• Improved testing, CI

Version 5.2.1

Changes

• Fixed test_find_clusters.R to accommodate variability in label assignments given by FindClusters across different systems (#9641)

Version 5.2.0

Changes

• Added group.by parameter to FindAllMarkers, allowing users to regroup their data using a non-default identity class prior to performing differential expression (#9550)
• Added image.type parameter to Read10X_Image enabling VisiumV1 instances to be populated instead of instances of the default VisiumV2 class (#9556)
• Fixed IntegrateLayers to respect the dims.to.integrate parameter
• Added stroke.size parameter to DimPlot (#8180)
• Updated RunLeiden to use the leidenbase package instead of leiden; deprecated the method parameter for RunLeiden and FindClusters; updated RunLeiden to reset random.seed to 1 if the value is 0 or less (#6792)
• Updated RunPCA to use the BPCells-provided SVD solver on BPCells matrices; updated JackStraw to support BPCells matrices (#8271)
• Fixed RunPCA to avoid converting BPCells matrices into dense matrices - significantly reduces the function's memory usage when running on BPCells matrices (#8966)
• Updated RunSLSI to support BPCells matrices
• Fixed DietSeurat so that the layers parameter is respected (#8197)
• Updated RunUMAP to support umap-learn version >= 0.5.0 (#9559)
• Updated LoadXenium and ReadXenium to accommodate the output from XOA v3.0; updated LoadXenium to provide more fine-grained control over the datatypes parsed in, including nucleus segmentation masks, segmentation methods, and other experimental metadata; updated ReadXenium to load cell_feature_matrix.h5 when present in favor of the MEX format files; updated ReadXenium to load .parquet files using arrow instead of .csv.gz files to support XOA 3.0 (#8604)
• Fixed LoadXenium to accommodate datasets without "Blank Codeword" or "Unassigned Codeword" matrices(#9135)
• Fixed ReadXenium to properly parse multiple molecular outputs at once (#8265)
• Added features parameter to LeverageScore and SketchData
• Updated SketchData's ncells parameter to accept integer vector

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