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Releases: satijalab/seurat

Version 4.0.6

16 Dec 17:01
8da35ba
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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

19 Oct 17:19
a556035
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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

27 Aug 13:35
13b615c
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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

11 Jun 19:19
9b38929
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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

24 May 16:36
af2925c
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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()

Version 4.0.1

18 Mar 16:02
4e868fc
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Changes

  • Equality added to differential expression thresholds in FindMarkers (e.g, >= logfc.threshold rather than >)
  • Read10X() now prepends dataset number for first dataset when reading multiple datasets
  • Bug fix for subset.AnchorSet()
  • Bug fix for fold change values in FindMarkers() when setting a different pseudocount (#4111)
  • Bug fix for RunLDA() related to proper passing of assay parameter.
  • When using order=TRUE in SingleDimPlot(), print NA points under all others.
  • Remove default parameter value for data.dir in Read10X()
  • Import spatstat fxns from subpackages (spatstat.core, spatstat.geom)
  • RunUMAP now checks for graph/neighbor consistency

Additions

  • Add direction option to PlotClusterTree()
  • Add cols parameter to JackStrawPlot()
  • Add ReadMtx() to read local and remote mtx files with associated cell and feature name files

Version 4.0.0

01 Feb 01:46
9843b84
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Changes

  • Removed old, deprecated code
  • Utilize SeuratObject as base of object code
  • Default neighbor finding algorithm changed from "rann" to "annoy"
  • Default ncells parameter in SCTransform() changed to 5000
  • Default fold change in FindMarkers() changed from ln to log2
  • Implementation improvements to AverageExpression()
  • AnchorSet class re-implemented as a virtual class from which IntegrationAnchorSet and TransferAnchorSet now inherit.
  • Point size in VlnPlot() now set automatically if not specified
  • Return the sample.tree properly when integrating with a single reference dataset
  • Replace as.character.quosure usage with as_label due to deprecation
  • Minor changes to the exact calculation of the anchor weight matrix
  • Default rasterization limit in DimPlot() and FeaturePlot() changed from 50,000 to 100,000
  • SCTransform() now returns a formalized Assay subclass SCTAssay()
  • When using normalization.method='SCT' in FindTransferAnchors(), normalize query using reference SCT model when possible.

Additions

  • Expose FoldChange() component in FindMarkers()
  • Add IntegrateEmbeddings() to correct embeddings of DimReducs
  • Add ProjectUMAP() to project query cells into a reference UMAP space
  • Add MapQuery() as a wrapper around IntegrateData(), IntegrateEmbeddings(), and ProjectUMAP()
  • Add MappingScore to compute a per-cell mapping score used in Azimuth
  • Add AggregateExpression() for summation based pseudobulk calculations
  • Add mixscape functionality via CalcPerturbSig(), PrepLDA(), RunLDA(), DEenrichRPlot(), MixscapeHeatmap(), MixscapeLDA(), PlotPerturbScore(), RunMixscape()
  • Add FindSubCluster() to further cluster existing clusters
  • Add supervised PCA functionality via RunSPCA()
  • Add functionality to enable weighted nearest neighbor analyses via FindMultiModalNeighbors()
  • Add neighbor visualization plot via NNPlot().
  • Add PredictAssay() to impute expression or embeddings from nearest neighbors
  • Add AnnotateAnchors() to aid in AnchorSet interpretation as well as subset.AnchorSet()
  • Add flexibility of choice for cell column in Read10X()
  • Add rasterization option to FeatureScatter() and VariableFeaturePlot()

Version 3.2.3

15 Dec 17:13
b56d194
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Deprecations

  • do.cpp parameter in IntegrateData and TransferData deprecated and will default to true

Changes

  • Same deprecated in favor of base::identity
  • Fix in DietSeurat to work with specialized Assay objects
  • Fix p-value return when using the ape implementation of Moran's I
  • Fix bug in FindMarkers when using MAST with a latent variable
  • Updates to Key<-.DimReduc that allow handling of empty reduction column names
  • Allow setting ctrl in CellCycleScoring
  • Modify subset.Seurat to allow specialized Assay subsetting methods
  • Fix image selection in interactive spatial plots
  • Update Rcpp functions with export(rng=FALSE) to avoid potential future warnings
  • Fix RenameCells bug for integrated SCT assays
  • Fix highlight order with proper factor levels when using SetHighlight in plots
  • Small change in CellRanger version detection logic of h5 file to improve robustness to outside tools.

Additions

  • Titles added to DimPlot when specifying group.by parameter
  • keep.scale parameter added to FeaturePlot to control scaling across multiple features and/or splits.
  • raster parameter in various scatter plots (eg. DimPlot, FeaturePlot, CellScatter) for plot-native rasterization instead of using AugmentPlot

Version 3.2.2

28 Sep 16:45
fe93b05
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Changes

  • Set the seed in WhichCells regardless of whether or not idents is passed
  • Retain Graph and Neighbor objects when subsetting only on features
  • Fix data.frame input to CreateAssayObject() when data.frame has no rownames.
  • Default annoy search to sequential if not using multicore future plans.
  • Require sctransform >= 0.3.0

Version 3.2.1

07 Sep 16:57
c23845d
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Deprecations

  • CreateActivityMatrix deprecated in favor of Signac::GeneActivity
  • ReadAlevin and ReadAlevinCsv deprecated in favor of SeuratWrappers::ReadAlevin
  • ExportToCellbrowser and StopCellbrowser deprecated in favor of SeuratWrappers::ExportToCellbrowser and SeuratWrappers::StopCellbrowser
  • ReadH5AD and WriteH5AD deprecated in favor of h5Seurat/H5AD functionality found in SeuratDisk
  • as.loom and as.Seurat.loom deprecated in favor of functionality found in SeuratDisk

Changes

  • Allow setting slot parameter in RunUMAP
  • Added support for FIt-SNE v1.2+
  • Fix for Spatial*Plot when running with interactive=TRUE
  • Set max for number of items returned by Top and remove duplicate items when balanced=TRUE
  • Fix logging bug when functions were run via do.call()
  • Fix handling of weight.by.var parameter when approx=FALSE in RunPCA()
  • Fix issue where feature names with dashes crashed CellSelector
  • Fix issue where errors in subsetting were being swallowed
  • Fix issue where labeling uncropped spatial plots was broken

Additions

  • Added support for nearest neighbor input and return.model parameter in RunUMAP()
  • Enable named color vectors in DoHeatmap()
  • Add label.color and label.box parameters to DimPlot
  • Added shuffle and seed parameters to DimPlot() to help with overplotting
  • Added new stacked violin plot functionality