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Releases: satijalab/seurat

Version 5.1.0

10 May 20:15
1549dcb
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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

19 Mar 12:27
c54e57d
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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

29 Feb 13:55
656fc8b
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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

21 Nov 20:56
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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

05 Nov 01:47
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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

28 Sep 14:06
d9f09de
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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

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

Version 4.3.0

05 Dec 22:50
763259d
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Added

  • Add support for imaging-based spatial datasets

Changes

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

Version 4.2.0

21 Oct 19:08
c463873
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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

02 May 14:00
a1294c4
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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

14 Jan 18:56
f1b2593
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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