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Seurat 5.1.0 (2024-05-08)

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

Seurat 5.0.3 (2024-03-18)

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

Seurat 5.0.2 (2024-02-28)

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)

Seurat 5.0.1 (2023-11-16)

Changes

• Fixed SCTransform.StdAssay to pass extra arguments to sctransform::vst(). Fixes #875
• 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

Seurat 5.0.0 (2023-10-25)

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

Seurat 4.4.0 (2023-09-27)

Added

• Add 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 bug in ReadMtx() to add back missing parameters
• Fix SCTransform() for V5 assays to retain gene attributes (#7557)
• Fix LeverageScore() for objects with few features (#7650

Seurat 4.3.0 (2022-11-18)

Added

• Add support for imaging-based spatial datasets

Changes

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

Seurat 4.2.1 (2022-11-08)

Changes

• Replaced import from spatstat.core with spatstat.explore
• Fix bug in FindMarkers() when using SCT assay (#6856)

Seurat 4.2.0 (2022-09-21)

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

Seurat 4.1.1 (2022-05-01)

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")

Seurat 4.1.0 (2022-01-14)

Added

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

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)

Seurat 4.0.6 (2021-12-16)

Added

• Implement supervised LSI

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)

Seurat 4.0.5 (2021-10-04)

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)
• Set random state in RunUMAP() when using the umap-learn method (#5194)

Seurat 4.0.4 (2021-08-19)

Added

• 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()
• Add support for the correlation metric in RunUMAP (#4972)

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()

Seurat 4.0.3 (2021-06-10)

Added

• Add jitter parameter to FeatureScatter()

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

Seurat 4.0.2 (2020-05-20)

Added

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

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.

Seurat 4.0.1 (2020-03-17)

Added

• 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

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

Seurat 4.0.0 (2020-01-27)

Added

• Expose FoldChange() component in FindMarkers().
• Add the merge.DimReduc method
• 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 Graphs() function to access the names of the stored Graph objects or pull a specific one
• Add checks for NA, NaN, logical, non-integer, and infinite values during CreateAssayObject and NormalizeData.default
• 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()
• Add step1 feature parameters in the SCTModel via PrepVSTResults()

Changes

• 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.
• Change default Neighbor name in FindNeighbors to Assay.nn

Removed

• CreateGeneActivityMatrix replaced by Signac::GeneActivity()
• RunLSI replaced by by Signac::RunTFIDF() and Signac::RunSVD()
• ReadAlevin and ReadAlevinCsv moved to SeuratWrappers
• ExportToCellbrowser and StopCellbrowser moved to SeuratWrappers

Seurat 3.2.3 - 2020-12-14

Added

• Titles added to DimPlot when specifying group.by parameter
• keep.scale parameter added to FeaturePlot to control scaling across multiple features and/or splits.

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.
• do.cpp deprecated and will default to true

Seurat 3.2.2 (2020-09-25)

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

Seurat 3.2.1 (2020-09-04)

Added

• 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

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

Deprecated

• 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

Seurat 3.2.0 (2020-07-15)

Added

• Added ability to create a Seurat object from an existing Assay object, or any object inheriting from the Assay class
• Added ability to cluster idents and group features in DotPlot
• Added ability to use RColorBrewer plaettes for split DotPlots
• Added visualization and analysis functionality for spatially resolved datasets (Visium, Slide-seq).

Changes

• Removed add.iter parameter from RunTSNE function
• Fixed integer overflow error in the WilcoxDETest function
• Minor visual fixes in DoHeatmap group bar + labels
• Efficiency improvements in anchor scoring (ScoreAnchors)
• Fix bug in FindClusters() when the last node has no edges
• Default to weighted = TRUE when constructing igraph objects in RunLeiden. Remove corresponding weights parameter from FindClusters().
• Fix handling of keys in FeatureScatter()
• Change CellSelector to use Shiny gadgets instead of SDMTools
• Mark PointLocator as defunct
• Remove SDMTools
• Fixed data slot return in AverageExpression when subsetting features and returning a Seurat object

Seurat 3.1.5 (2020-04-14)

Added

• New scale parameter in DotPlot
• New keep.sparse parameter inCreateGeneActivityMatrix` for a more memory efficient option
• Added ability to store model learned by UMAP and project new data
• New strip.suffix option in Read10X. This changes the default behavior of Read10X. A trailing -1 present in all cell names will not be removed by default.
• Added group.by parameter to FeatureScatter

Changes

• Replace wilcox.test with limma implementation for a faster FindMarkers default method
• Better point separation for VlnPlots when using the split.by option
• Efficiency improvements for anchor pairing
• Deprecate redundant sort.cell parameter in FeaturePlot
• Fixes to ensure correct class of Matrix passed to c++ functions
• Fixes for underscores in ident labels for DotPlot
• Ensure preservation of matrix dimnames in SampleUMI
• Fix non-standard evaluation problems in subset and WhichCells
• Default split violin option is now a multi group option
• Preserve alpha in FeaturePlot when using blend
• Update assay.used slot for DimReducs when Assay is renamed

Seurat 3.1.4 (2020-02-20)

Changes

• Fixes to DoHeatmap to remain compatible with ggplot2 v3.3
• Adoption of patchwork framework to replace CombinePlots

Seurat 3.1.3 (2020-02-07)

Added

• New system agnostic Which function to address problems with FItSNE on Windows

Changes

• Export CellsByIdentities and RowMergeSparseMatrices functions
• nCount and nFeature metadata variables retained after subset and updated properly with UpdateSeuratObject
• Fix uwot support for running directly on feature matrices
• Fixes for keys with underscores
• Fix issue with leiden option for FindClusters
• Fix for data transfer when using sctransform
• SDMTools moved to Suggests as package is orphaned

Seurat 3.1.2 (2019-12-11)

Added

• New silent slot updater
• New random seed options to RunCCA, RunTSNE, WhichCells, HTODemux, AddModuleScore, VlnPlot, and RidgePlot
• Enhancements for dealing with Assay-derived objects

Changed

• Only run CalcN (generates nFeatures and nCounts) when counts changes
• Fix issue regarding colons in feature names
• Change object class testing to use inherits or is.* for R 4.0 compatability

Seurat 3.1.1 (2019-09-20)

Added

• New RegroupIdents function to reassign idents based on metadata column majority
• UpdateSymbolList function to pull new gene names from HGNC
• Added support for H5AD layers as additional assays in a Seurat object

Changed

• Fix rownames issue when running UMAP on dist object
• Add support for new H5AD obsm and varm stucture
• Fix issue when trying to read non-existent feature-level metadata from an H5AD file
• Fix in integration workflow when using SCTransform
• Improved error checking for AddModuleScore
• cbind fix in reference-based integration (MapQuery)
• Fix for convenience plots error hanging
• Ensure Seurat objects aren’t stored in the command logs

Seurat 3.1.0 (2019-08-20)

Added

• New PrepSCTIntegration function to facilitate integration after SCTransform
• Reference-based integration with the reference parameter in FindIntegrationAnchors
• Reciprocal PCA as a reduction option in FindIntegrationAnchors
• New CollapseEmbeddingOutliers function
• Enable FindTransferAnchors after SCTransform
• Added back ColorDimSplit functionality
• Include a code of conduct
• Added uwot support as new default UMAP method
• Added CheckDots to catch unused parameters and suggest updated names
• Reductions and Assays assays functions to list stored DimReducs and Assays

Changed

• Fix regex in LogSeuratCommand
• Check for NAs in feature names in Read10X
• Prevent dimnames for counts/data/scale.data matrices from being arrays
• Updates ReadH5AD to distinguish FVF methods
• Fixes to UpdateSeuratObject for v2 objects
• Sink all output from stdout to stderr
• Fix to scale.data cell ordering after subsetting
• Enable Assay specification in BuildClusterTree
• Fix FeaturePlot when using both blend and split.by
• Fix to WhichCells when passing cells and invert
• Fix to HoverLocator labels and title
• Ensure features names don’t contain pipes (|)
• Deprecation of RunLSI and RunALRA
• Fix legend bug when sorting in ExIPlot

Seurat 3.0.2 (2019-06-07)

Added

• Flag to skip singleton grouping in FindClusters
• New custom colors for blended FeaturePlots
• New GetResidual function
• New Seurat/Monocle converters

Changed

• Fix issue where certain assays weren’t being shown in the Seurat object
• Fix issue where we weren’t updating DimReduc object column names
• Fix line spacers in DoHeatmap
• Fix uninformative labels in FeaturePlot
• Fix unset identities when converting from SCE to Seurat
• Fix single colors being interpreted as palettes in SingleDimPlot
• Ensure factor levels are always numerically increasing after FindClusters
• Better cell highlighting colors for DimPlot
• Fix to levels<-.Seurat
• Add ability to use counts/scaled data in BuildClusterTree
• Minor fix to split ScaleData

Seurat 3.0.1 (2019-05-16)

Added

• Add global option (Seurat.memsafe) to skip gc() calls
• Restore draw.lines to DoHeatmap, maintain size of color bar with different number of features (#1429)
• Enable split.by parameter for ScaleData
• Add slot parameter to FeaturePlot (#1483)
• Add assay parameter to DotPlot (#1404)

Changed

• Fix to color options for VlnPlot with split.by option (#1425)
• Improvements to conversion functions (loom, SCE)
• Fix for cluster tree reordering (#1434)
• Fix PercentageFeatureSet for single feature case
• Fix to fold change calculation and filtering for other slots in FindMarkers (#1454)
• Keep title vectorized in AugmentPlot (#1515)
• Export LogSeuratCommand function
• Fix for FindConservedMarkers when one ident is missing from a group (#1517)

Seurat 3.0.0 (2019-04-16)

Added

• New method for identifying anchors across single-cell datasets
• Parallelization support via future
• Additional method for demultiplexing with MULTIseqDemux
• Support normalization via sctransform
• New option for clustering with the Leiden algorithm
• Support for reading 10X v3 files
• New function to export Seurat objects for the UCSC cell browser
• Support for data import from Alevin outputs
• Imputation of dropped out values via ALRA

Changed

• Significant code restructuring
• Most occurances of “gene(s)” in function names/arguments renamed to “feature(s)”
• Changes to the Seurat object class to facilitate multimodal data
• New BlendPlot implementation

Seurat 2.3.4 (2018-07-13)

Added

• GetIdent function added to pull identity info

Changed

• DiffusionMap dependency replaced with destiny to avoid archival
• Java dependency removed and functionality rewritten in Rcpp
• Speed and efficiency improvements for Rcpp code
• More robust duplicate handling in CellCycleScoring

Seurat 2.3.3 (2018-07-02)

Added

• New HTOHeatmap function
• Support for custom PNG arguments for vector-friendly plotting
• Fix for ‘NA’-labeled cells disappearing with custom color scale

Changed

• Replaced FNN with RANN
• Removed unused compiler flags
• Moved several lightly-used packages from ‘imports’ to ‘suggests’

Seurat 2.3.2 (2018-06-11)

Added

• RenameCells added for easy renaming of all cells
• Read10X_h5 added to read in 10X formatted h5 files
• SetAssayData ensures cell order is the same between assay objects and the Seurat object
• Compatability updates for ggplot2 v2.3.0

Seurat 2.3.1 (2018-05-03)

Added

• Support for UMAP dimensional reduction technique
• New conversion functions for SingleCellExperiment and anndata

Changed

• FetchData preserves cell order
• Require Matrix 1.2-14 or higher
• AddModuleScore no longer densifies sparse-matrices
• Various visualization fixes and improvements
• Default value for latent.vars in FindMarkers/FindAllMarkers changed to NULL.

Seurat 2.3.0 (2018-03-22)

Added

• Support for HTO demultiplexing
• Utility functions: TransferIdent, CombineIdent, SplitObject, vector.friendly
• C++ implementation for parts of BuildSNN
• Preliminary parallelization support (regression and JackStraw)
• Support for FItSNE

Changed

• MetaDE replaced with metap for combining p-values (MetaDE was removed from CRAN)
• NMF heatmaps replaced (NMF to be archived by CRAN)

Seurat 2.2.1 (2018-02-14)

Changed

• MetaDE replaced with metap for combining p-values (MetaDE was removed from CRAN)
• NMF heatmaps replaced (NMF to be archived by CRAN)

Seurat 2.2.0 (2018-01-10)

Added

• Multiple alignment functionality with RunMultiCCA and AlignSubspace extended to multiple datasets
• CalcAlignmentScore added to evaluate alignment quality
• MetageneBicorPlot added to guide CC selection
• Change cluster order in DoHeatmap with group.order parameter
• Ability to change plotting order and add a title to DimPlot
• do.clean and subset.raw options for SubsetData

Changed

• JoyPlot has been replaced with RidgePlot
• FindClusters is now more robust in making temp files
• MetaDE support for combining p-values in DE testing

Seurat 2.1.0 (2017-10-12)

Added

• Support for using MAST and DESeq2 packages for differential expression testing in FindMarkers
• Support for multi-modal single-cell data via @assay slot

Changed

• Default DE test changed to Wilcoxon rank sum test

Seurat 2.0.1 (2017-08-18)

Added

• Now available on CRAN
• Updated documentation complete with examples
• Example datasets: pbmc_small and cc.genes
• C++ implementation for parts of FindVariableGenes
• Minor bug fixes

Seurat 2.0.0 (2017-07-26)

Added

• New method for aligning scRNA-seq datasets
• Significant code restructuring
• New methods for scoring gene expression and cell-cycle phases
• New visualization features (do.hover, do.identify)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.