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Seurat 5.4.0

Additions

• Added support for 10x Space Ranger 4.0 outputs (Visium data withsegmentations)
  • Updated data loading functionsLoad10X_Spatial,Read10X_Image,
  • UpdatedGetTissueCoordinates.VisiumV2
  • Updated spatial visualization functionsSpatialPlot,SingleSpatialPlot,SpatialDimPlot,SpatialFeaturePlot
  • Added helper functionsRead10X_Segmentations,Read10X_HD_GeoJson,Format10X_GeoJson_CellID
• Added functionInteractiveSpatialPlot to allow users tointeractively 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 fordetails
  • For binned Visium data,x now correctly corresponds toimagecol from tissue positions;y nowcorrectly corresponds toimagerow from tissue positions;these are now consistent with 10X’s coordinate system (with the originbeing the top left).
• Reverted#10062 infavor of fetching both grouping variables and dimensionality reductionembeddings withFetchData as previously; added warning toalert users when column names of metadata and dimensionality reductionembeddings conflict
• Added color retrieval logic inLabelClusters forconsistent cluster label coloring (#10198)

Seurat 5.3.1

Changes

Additions

• Added option to usecluster_leiden fromigraph when running Leiden clustering (#9931)
• Added option to useumap2 fromuwot whenrunning UMAP (#9918)
• Added option to useapprox_pow parameter fromuwot when running UMAP (#9449)
• UpdatedLoadXenium to add support for Xenium proteindata (#10024)
• Added option to specify stroke size inFeaturePlot (#10053)
• Addedlabel.size.cutoff parameter toDimPlot to allow users to label only clusters above acertain size (#10092)

Fixes

• Fixed deprecated calls to Seurat functionsGetAssayDataandPackageCheck (#9924), (#10102)
• Fixed errors inRunAzimuth relating toFindTransferAnchors (#9924)
• Fixed errors inLeverageScore relating to handling of(variable) features (#9924)
• UpdatedPseudobulkExpression to acccount for the casethat a category passed togroup.by has only one value (#10092)
• UpdatedVlnPlot to use assay passed to the function ifspecified (#10092)
• UpdatedFeatureScatter to allow gene names withparentheses to be plotted (#10092)
• UpdatedSingleRasterMap to store object metadatacorrectly (#10092)
• UpdatedFindClusters to order cluster factor levelscorrectly when assigning a custom cluster name (#10092)
• UpdatedFindConservedMarkers to remove NA values (#9917)
• Updated visualization functions to avoid ggplot2guides,aes_string, andfacet_grid deprecation warnings (#9409,#10116)
• FixedDimPlot bug where metadata columns named ‘PC_1’,‘UMAP_1’ etc override reduction embeddings (#10062)

Seurat 5.3.0

Changes

• FixedPseudobulkExpression to forward relevantarguments toNormalizeData (#9840)
• Fixed bugs inFindSpatiallyVariableFeatures; deprecatedtheslot parameter in favor oflayer (#9836)
• ExtendedFindTransferAnchors’sreferenceargument to accept SCT inputs containing more than one SCT model; inthis case, the reference model that was fit against the largest numberof cells is used (#9833)
• ExtendedFindTransferAnchors’squeryargument to accept multi-layer inputs; updatedMappingScoreto support multi-layer query inputs (#9832)
• UpdatedLeverageScore.default to convertBPCells::IterableMatrix inputs with less than 7500 cellsinto a sparse matrix before performing the calculation (#9831)
• DroppedVariableFeatures setter fromSketchData (#9830)
• ExtendedCells.SCTAssay’slayer argumentaccept slot names:"counts","data","scale.data"; enabled compatibility withSketchData/LeverageScore(#9830)
• UpdatedSCTransform.StdAssay to simplify and speed upthe method (#9828)
• UpdatedAddModuleScore to support multi-layer inputs(#9826)
• FixedPseudobulkExpression to work withSeurat inputs containing more than one assay (9824)
• AddedRunICA.StdAssay (#9825)
• UpdatedHarmonyIntegration to callharmony::RunHarmony in favor of the deprecatedharmony::HarmonyMatrix (#9789)
• Addedraster.dpi parameter toVlnPlot (#9665)
• FixedSpatialDimPlot(..., interactive = TRUE) tosupportSlideSeq andSTARmap input types;addedScaleFactors.SlideSeq &ScaleFactors.STARmap generics (#9691)
• FixedPercentageFeatureSet so that theassay parameter is always respected; fixedPercentageFeatureSet to raise a warning if anyfeatures are absent in the specifiedassayinstead of throwing an error (#9686)
• FixedGroupCorrelation andGroupCorrelationPlot to be compatible withSeuratObject >= 5.0.0 (#9625)

Seurat 5.2.1 (2025-01-23)

Changes

• Fixedtest_find_clusters.R to accommodate variabilityin label assignments given byFindClusters across differentsystems (#9641)

Seurat 5.2.0 (2024-12-20)

Changes

• Addedgroup.by parameter toFindAllMarkers, allowing users to regroup their data usinga non-default identity class prior to performing differential expression(#9550)
• Addedimage.type parameter toRead10X_Image enablingVisiumV1 instances tobe populated instead of instances of the defaultVisiumV2class (#9556)
• FixedIntegrateLayers to respect thedims.to.integrate parameter
• Addedstroke.size parameter toDimPlot (#8180)
• UpdatedRunLeiden to use theleidenbasepackage instead ofleiden; deprecated themethod parameter forRunLeiden andFindClusters; updatedRunLeiden to resetrandom.seed to 1 if the value is 0 or less (#6792)
• UpdatedRunPCA to use theBPCells-providedSVD solver onBPCells matrices; updatedJackStraw to supportBPCells matrices (#8271)
• FixedRunPCA to avoid convertingBPCellsmatrices into dense matrices - significantly reduces the function’smemory usage when running onBPCells matrices (#8966)
• UpdatedRunSLSI to supportBPCellsmatrices
• FixedDietSeurat so that thelayersparameter is respected (#8197)
• UpdatedRunUMAP to supportumap-learnversion >= 0.5.0 (#9559)
• UpdatedLoadXenium andReadXenium toaccommodate the output fromXOA v3.0; updatedLoadXenium to provide more fine-grained control over thedatatypes parsed in, including nucleus segmentation masks, segmentationmethods, and other experimental metadata; updatedReadXenium to load cell_feature_matrix.h5 when present infavor of the MEX format files; updatedReadXenium to load.parquet files usingarrow instead of .csv.gz files tosupport XOA 3.0 (#8604)
• FixedLoadXenium to accommodate datasets without “BlankCodeword” or “Unassigned Codeword” matrices(#9135)
• FixedReadXenium to properly parse multiple molecularoutputs at once (#8265)
• Addedfeatures parameter toLeverageScoreandSketchData
• UpdatedSketchData’sncells parameter toaccept integer vector

Seurat 5.1.0 (2024-05-08)

Changes

• Updated interactiveSpatialDimPlots to display spatialcoordinates
• UpdatedBuildClusterTree toPseudobulkExpression(..., method = "aggregate") instead ofAverageExpression
• FixedSpatialPlot to properly handle images with sharedcells
• Addedcluster.name parameter toBuildNicheAssay
• AddedVisiumV2 class, inheritsSeuratObject::FOV, returned byLoad10X_Spatial
• UpdatedLoad10X_Spatial to support loading Visium HDdatasets - addedbin.size parameter
• UpdatedRead10X_Coordinates to handle newtissue_coordinates.parquet files
• Addedshape parameter toSpatialPlot andwrappers:SpatialFeaturePlot andSpatialDimPlot
• Addedimage.scale parameter toSpatialPlotand related functions:SpatialFeaturePlot/ISpatialFeaturePlot andSpatialDimPlot/ISpatialDimPlot
• Restoredimage.name parameter toRead10X_Image
• Addedscale parameter toRadius.VisiumV1
• Fixed calculation ofspot.radius attribute forVisiumV1 instance returned byRead10X_Image —replacescale.factors$fiducial withscale.factors$spot
• AddedRead10X_Coordinates andRead10X_ScaleFactors
• FixedSpatialPlot to properly handle mutli-assaySeurat instances

Seurat 5.0.3 (2024-03-18)

Changes

• FixedPercentAbove to discount null values (#8412)
• Addedlog parameter toFeatureScatter
• Fixed handling ofclip.range forSCTransform whenncells is less than the sizeof the passed dataset

Seurat 5.0.2 (2024-02-28)

Changes

• FixedAverageExpression to handlefeaturesvector whenlayer="scale.data" andreturn.seurat=TRUE
• Addedfc.slot parameter toFindMarkers
• FixedSCTransform to handlevars.to.regress (#8148) and(#8349)
• FixedSCTransform to handle fetching residuals (#8185)

Seurat 5.0.1 (2023-11-16)

Changes

• FixedSCTransform.StdAssay to pass extra arguments tosctransform::vst(). Fixes#875
• Fixed PercentageFeatureSet Layer calling(#8009)
• Fixed cell highlighting(#7914)
• Updated marker sorting to be by p-value with ties broken by absolutedifference in percent expression
• Fixed issue with replicated barcodes in MappingScore(#7922)
• ImprovedPseudobulkExpression by adding ‘g’ to cellnames that started with numeric values
• ImprovedPseudobulkExpression by adding each variablespecified ingroup.by as columns in the object metadatawhenreturn.seurat=TRUE
• FixedDimPlot andFeatureScatter whichwere breaking when using thesplit.by argument with avariable that contained NAs

Seurat 5.0.0 (2023-10-25)

Added

• AddBridgeCellsRepresentation to construct a dictionaryrepresentation for each unimodal dataset.
• AddBuildNicheAssay to construct a new assay where eachfeature is a cell label. The values represent the sum of a particularcell label neighboring a given cell.
• AddCalcDispersion to calculate the dispersion offeatures.
• AddCCAIntegration to perform Seurat-CCAIntegration.
• AddCountSketch to generate a CountSketch randommatrix.
• AddCreateCategoryMatrix to create a one-hot matrix fora given label.
• AddDISP to find variable features based ondispersion.
• AddFastRPCAIntegration as a convenience wrapperfunction around the following three functions that are often runtogether when performing integration.
• AddFetchResiduals_reference as a temporary function toget residuals from the reference.
• AddFetchResiduals to callsctransform::get_residuals.
• AddFetchResidualSCTModel to calculate Pearsonresiduals of features not in the scale.data.
• AddFindBridgeAnchor to find bridge anchors between twounimodal datasets.
• AddFindBridgeIntegrationAnchors to find a set ofanchors for integration between unimodal query and the other unimodalreference using a pre-computed BridgeReferenceSet.
• AddFindBridgeTransferAnchors to find a set of anchorsfor label transfer between unimodal query and the other unimodalreference using a pre-computed BridgeReferenceSet.
• AddGaussianSketch to perform Gaussian sketching.
• AddHarmonyIntegration to perform Harmonyintegration.
• AddIntegrateLayers to integrate layers in an assayobject.
• AddJointPCAIntegration to perform Seurat-Joint PCAIntegration.
• AddLeverageScore to compute the leverage scores for agiven object.
• AddLoadCurioSeeker to load Curio Seeker data.
• AddMVP to find variable features based onmean.var.plot.
• AddNNtoGraph to convert the Neighbor class to anasymmetrical Graph class.
• AddPrepareBridgeReference to preprocess the multi-omicbridge and unimodal reference datasets into an extended reference.
• AddProjectCellEmbeddings to project query data ontothe reference dimensional reduction.
• AddProjectData to project high-dimensional single-cellRNA expression data from a full dataset onto the lower-dimensionalembedding of the sketch of the dataset.
• AddProjectDimReduc to project query data to referencedimensional reduction.
• AddProjectIntegration to integrate embeddings from theintegrated sketched.assay.
• AddPseudobulkExpression to normalize the count datapresent in a given assay.
• AddRead10X_probe_metadata to read the probe metadatafrom a 10x Genomics probe barcode matrix file in HDF5 format.
• AddRPCAIntegration to perform Seurat-RPCAIntegration.
• AddRunGraphLaplacian to run a graph Laplaciandimensionality reduction.
• AddSelectIntegrationFeatures5 to select integrationfeatures for v5 assays.
• AddSelectSCTIntegrationFeatures to select SCTintegration features.
• AddSketchData to use sketching methods to downsamplehigh-dimensional single-cell RNA expression data for help withscalability for large datasets.
• AddTransferSketchLabels to transfer cell type labelsfrom a sketched dataset to a full dataset based on the similarities inthe lower-dimensional space.
• AddUnSketchEmbeddings to transfer embeddings fromsketched cells to the full data.
• AddVST to apply a variance stabilizing transformationfor selection of variable features.

Changes

• ChangeFindTransferAnchors so that anchor filtering isnot performed by default
• Changemerge so that layers will be added to a singleSeurat object instead of combining raw count matrices
• Deprecateslot parameter in favor oflayers in accessor and set methods

Seurat 4.4.0 (2023-09-27)

Added

• Add parallelization support with speed improvements forPrepSCTFindMarkers
• Fix bug inLoadNanostring(#7566)

Changes

• Fix bug inas.Seurat.SingleCellExperiment() (#6692)
• Support for Visium probe information introduced in Spaceranger 2.1(#7141)
• AddLoadCurioSeeker to load sequencing-based spatialdatasets generated using the Curio Seeker
• Fix fold change calculation for assays (#7095)
• Fixpt.size bug when rasterization is set to true (#7379)
• FixFoldChange andFindMarkers to supportall normalization approaches (#7115,#7110,#7095,#6976,#6654,#6701,#6773,#7107)
• Fix for handling newer ParseBio formats inReadParseBio(#7565)
• Fix for handling rasterization by default (#7842)
• Fix bug inReadMtx() to add back missingparameters
• FixSCTransform() for V5 assays to retain geneattributes (#7557)
• FixLeverageScore() for objects with few features (#7650

Seurat 4.3.0 (2022-11-18)

Added

• Add support for imaging-based spatial datasets

Changes

• Fix bug inFindMarkers() when run postIntegration/Transfer (#6856)

Seurat 4.2.1 (2022-11-08)

Changes

• Replaced import fromspatstat.core withspatstat.explore
• Fix bug inFindMarkers() when usingSCTassay (#6856)

Seurat 4.2.0 (2022-09-21)

Changes

• Fix legend color inDoHeatmap() (#5783)
• Fix bug inScaleData() when regressing out one gene (#5970)
• Fix name pulling inPlotPerturbScore() (#6081)
• Support spaceranger 2.0 (#6208)
• Fix bug inSpatialDimPlot() when usinggroup.by (#6179)
• Addadd.noise parameter inVlnPlot() (#5756)
• Fix uwot model backwards compatibility (#6345)
• Allowpseudocount.use in differential expressionfunctions to be set at theAssay level

Seurat 4.1.1 (2022-05-01)

Changes

• FixgiveCsparse related warnings inRead10X_h5
• Fix ident labeling forSpatialPlot (#5774)
• FixReadMtx on Windows (#5687)
• FixVlnPlot to switch on rasterization only whenrequired (#5846)
• Fixncol behavior inSpatialPlot (#5774)
• Setjitter to FALSE inFeatureScatter (#5876)
• UpdateCells methods to new signature(x, ...)
• Replace use ofdefault.stringsAsFactors() withgetOption("stringsAsFactors")

Seurat 4.1.0 (2022-01-14)

Added

• Addraster.dpi parameter toDimPlot/FeaturePlot to optionally rasterize individualpoints (#5392)
• Add support for sctransform v2, differential expression with SCTassay

Changes

• UpdateReadParseBio to support split-pipe 0.9.6p (#5446)
• Fixes for MAST differential expression (#5441)
• Fix scaling options when usingsplit.by inFeaturePlot() (#5243)

Seurat 4.0.6 (2021-12-16)

Added

• Implement supervised LSI

Changes

• Addraster parameter toVlnPlot tooptionally rasterize individual points (#5076)
• Addmin.cells.group parameter toFindConservedMarkers (#5079)
• Setdo.center to FALSE forlsiproject inFindTransferAnchors
• Fix error message inReadMtx() (#5158)
• Addlabel.color parameter toFeaturePlot(#5314)
• Fix issues inProjectUMAP (#5257,#5104,#5373)

Seurat 4.0.5 (2021-10-04)

Changes

• Update documentation forto.upper parameter inLoad10X_Spatial() (#4576)
• Update concept tags forRunSPCA() (#4978)
• Conditionally run tests/packages that use suggested packages (#5160)
• Set random state inRunUMAP() when using theumap-learn method (#5194)

Seurat 4.0.4 (2021-08-19)

Added

• Addreduction parameter toBuildClusterTree() (#4598)
• Add DensMAP option toRunUMAP() (#4630)
• Addimage parameter toLoad10X_Spatial()andimage.name parameter toRead10X_Image()(#4641)
• AddReadSTARsolo() function to read output fromSTARsolo
• Adddensify parameter toFindMarkers()
• AddReadParsebio() function to read output from ParseBiosciences
• Add theimage.alpha parameter toSpatialDimPlot() andSpatialFeaturePlot()
• Add support for the correlation metric inRunUMAP (#4972)

Changes

• Warn and continue rather than erroring if not all features areavailable inFindSpatiallyVariableFeatures() (#4611)
• Bug fix for SCT-based integration in selecting proper referencemodel (#4355)
• Bug fix for reading from absolute paths in ReadMtx (#4723)
• Bug fix in SingleCellExperiment conversion (#4633)
• Bug fix inFindVariableFeatures() when usingselection.method = "mvp" andbinning.method = "equal_frequency" (#4712)
• Bug fix inDoHeatmap() to remove random characters fromplot legend(#4660)
• Fix cell renaming inRunCCA()
• Fix issue in SingleCellExperiment conversion where the mainExp wouldnot be set properly
• Fix for default dispersion info displayed inVariableFeaturePlot()

Seurat 4.0.3 (2021-06-10)

Added

• Addjitter parameter toFeatureScatter()

Changes

• Fix issues withas.SingleCellExperiment.Seurat() forthe latest verion of SingleCellExperiment (#4532)
• Ensure proper reference.reduction is used inMapQuery()
• Fix toUpdateSymbolList(), no longer searches aliasesand exposes thesearch.types parameter inGeneSymbolThesarus() (#4545)
• Transferscale.data slot as well when converting withas.SingleCellExperiment.Seurat()
• Enablealpha parameter forSpatialDimPlot()
• Fixas.SingleCellExperiment.Seurat() conversion foratypicalreducedDim components

Seurat 4.0.2 (2020-05-20)

Added

• NewAddAzimuthScores() andAddAzimuthResults() functions
• Addshuffle parameter toFeatureScatter()(#4280)
• Addlsiproject andrpca options forFindTransferAnchors()
• Addrlsi option forFindIntegrationAnchors()

## Changes

• Preserve feature metadata when converting fromSingleCellExperiment toSeuratObject class (#4205)
• Preserve multiple assays when converting fromSingleCellExperiment toSeuratObject class (#3764)
• Fix passing ofscore.thresh parameter inScoreJackStraw() (#4268)
• Fix FC calculation inFindMarkers() non-log transformeddata.
• Add umap-learn version >= 0.5.0 compatibility forRunUMAP()
• FixDotPlot to uselog1p whenscale=False (#4298)
• Fix split and shuffledDimPlot
• Disallow NULL or another length 0 vector forident.1 inFindMarkers()
• Fix range shift when labeling clusters on a GeomSpatial plot
• Fix SpatialPlot distortion for non-square images.
• Fix future-related warnings inFindIntegrationAnchors()
• Fixfc.name parameter inFindMarkers() (#4474)
• Deprecategroup.by parameter inPlotPerturbScore() in favor ofmixscape.class.

Seurat 4.0.1 (2020-03-17)

Added

• Add direction option toPlotClusterTree()
• Addcols parameter toJackStrawPlot()
• AddReadMtx() to read local and remote mtx files withassociated cell and feature name files

Changes

• Equality added to differential expression thresholds inFindMarkers (e.g, >= logfc.threshold rather than>)
• Read10X() now prepends dataset number for first datasetwhen reading multiple datasets
• Bug fix forsubset.AnchorSet()
• Bug fix for fold change values inFindMarkers() whensetting a different pseudocount (#4111)
• Bug fix forRunLDA() related to proper passing of assayparameter.
• When usingorder=TRUE inSingleDimPlot(),print NA points under all others.
• Remove default parameter value fordata.dir inRead10X()
• Import spatstat fxns from subpackages (spatstat.core,spatstat.geom)
• RunUMAP now checks for graph/neighbor consistency

Seurat 4.0.0 (2020-01-27)

Added

• ExposeFoldChange() component inFindMarkers().
• Add themerge.DimReduc method
• AddIntegrateEmbeddings() to correct embeddings ofDimReducs
• AddProjectUMAP() to project query cells into areference UMAP space
• AddMapQuery() as a wrapper aroundIntegrateData(),IntegrateEmbeddings(), andProjectUMAP()
• AddMappingScore to compute a per-cell mapping scoreused in Azimuth
• AddAggregateExpression() for summation basedpseudobulk calculations
• Add mixscape functionality viaCalcPerturbSig(),PrepLDA(),RunLDA(),DEenrichRPlot(),MixscapeHeatmap(),MixscapeLDA(),PlotPerturbScore(),RunMixscape()
• AddFindSubCluster() to further cluster existingclusters
• Add supervised PCA functionality viaRunSPCA()
• Add functionality to enable weighted nearest neighbor analyses viaFindMultiModalNeighbors()
• Add neighbor visualization plot viaNNPlot().
• AddPredictAssay() to impute expression or embeddingsfrom nearest neighbors
• AddGraphs() function to access the names of the storedGraph objects or pull a specific one
• Add checks for NA, NaN, logical, non-integer, and infinite valuesduring CreateAssayObject and NormalizeData.default
• AddAnnotateAnchors() to aid in AnchorSetinterpretation as well assubset.AnchorSet()
• Add flexibility of choice for cell column inRead10X()
• Add rasterization option toFeatureScatter() andVariableFeaturePlot()
• Add step1 feature parameters in the SCTModel viaPrepVSTResults()

Changes

• Default neighbor finding algorithm changed from “rann” to“annoy”
• Defaultncells parameter inSCTransform()changed to 5000
• Default fold change inFindMarkers() changed from ln tolog2
• Implementation improvements toAverageExpression()
• AnchorSet class re-implemented as a virtual class fromwhichIntegrationAnchorSet andTransferAnchorSet now inherit.
• Point size inVlnPlot() now set automatically if notspecified
• Return the sample.tree properly when integrating with a singlereference dataset
• Replaceas.character.quosure usage withas_label due to deprecation
• Minor changes to the exact calculation of the anchor weightmatrix
• Default rasterization limit inDimPlot() andFeaturePlot() changed from 50,000 to 100,000
• SCTransform() now returns a formalizedAssay subclassSCTAssay()
• When usingnormalization.method='SCT' inFindTransferAnchors(), normalize query using reference SCTmodel when possible.
• Change default Neighbor name inFindNeighbors toAssay.nn

Removed

• CreateGeneActivityMatrix replaced bySignac::GeneActivity()
• RunLSI replaced by bySignac::RunTFIDF()andSignac::RunSVD()
• ReadAlevin andReadAlevinCsv moved toSeuratWrappers
• ExportToCellbrowser andStopCellbrowsermoved to SeuratWrappers

Seurat 3.2.3 - 2020-12-14

Added

• Titles added toDimPlot when specifyinggroup.by parameter
• keep.scale parameter added toFeaturePlotto control scaling across multiple features and/or splits.

Changes

• Same deprecated in favor ofbase::identity
• Fix inDietSeurat to work with specializedAssay objects
• Fix p-value return when using theape implementation ofMoran’s I
• Fix bug in FindMarkers when using MAST with a latent variable
• Updates toKey<-.DimReduc that allow handling ofempty reduction column names
• Allow settingctrl inCellCycleScoring
• Modify subset.Seurat to allow specialized Assay subsettingmethods
• Fix image selection in interactive spatial plots
• Update Rcpp functions withexport(rng=FALSE) to avoidpotential future warnings
• Fix RenameCells bug for integrated SCT assays
• Fix highlight order with proper factor levels when usingSetHighlight in plots
• Small change in CellRanger version detection logic of h5 file toimprove robustness to outside tools.
• do.cpp deprecated and will default to true

Seurat 3.2.2 (2020-09-25)

Changes

• Set the seed inWhichCells regardless of whether or notidents is passed
• Retain Graph and Neighbor objects when subsetting only onfeatures
• Fix data.frame input toCreateAssayObject() whendata.frame has no rownames.
• Default annoy search to sequential if not using multicore futureplans.
• Require sctransform >= 0.3.0

Seurat 3.2.1 (2020-09-04)

Added

• Added support for nearest neighbor input andreturn.model parameter inRunUMAP()
• Enable named color vectors inDoHeatmap()
• Addlabel.color andlabel.box parameterstoDimPlot
• Addedshuffle andseed parameters toDimPlot() to help with overplotting
• Added new stacked violin plot functionality

Changes

• Allow settingslot parameter inRunUMAP
• Added support for FIt-SNE v1.2+
• Fix forSpatial*Plot when running withinteractive=TRUE
• Set max for number of items returned byTop and removeduplicate items when balanced=TRUE
• Fix logging bug when functions were run viado.call()
• Fix handling of weight.by.var parameter when approx=FALSE inRunPCA()
• Fix issue where feature names with dashes crashedCellSelector
• Fix issue where errors in subsetting were being swallowed
• Fix issue where labeling uncropped spatial plots was broken

Deprecated

• CreateActivityMatrix deprecated in favor ofSignac::GeneActivity
• ReadAlevin andReadAlevinCsv deprecated infavor ofSeuratWrappers::ReadAlevin
• ExportToCellbrowser andStopCellbrowserdeprecated in favor ofSeuratWrappers::ExportToCellbrowserandSeuratWrappers::StopCellbrowser
• ReadH5AD andWriteH5AD deprecated in favorof h5Seurat/H5AD functionality found in SeuratDisk
• as.loom andas.Seurat.loom deprecated infavor of functionality found in SeuratDisk

Seurat 3.2.0 (2020-07-15)

Added

• Added ability to create a Seurat object from an existing Assayobject, or any object inheriting from the Assay class
• Added ability to cluster idents and group features inDotPlot
• Added ability to use RColorBrewer plaettes for splitDotPlots
• Added visualization and analysis functionality for spatiallyresolved datasets (Visium, Slide-seq).

Changes

• Removedadd.iter parameter fromRunTSNEfunction
• Fixed integer overflow error in the WilcoxDETest function
• Minor visual fixes inDoHeatmap group bar + labels
• Efficiency improvements in anchor scoring(ScoreAnchors)
• Fix bug inFindClusters() when the last node has noedges
• Default to weighted = TRUE when constructing igraph objects inRunLeiden. Remove corresponding weights parameter fromFindClusters().
• Fix handling of keys inFeatureScatter()
• ChangeCellSelector to use Shiny gadgets instead ofSDMTools
• MarkPointLocator as defunct
• RemoveSDMTools
• Fixed data slot return inAverageExpression whensubsetting features and returning a Seurat object

Seurat 3.1.5 (2020-04-14)

Added

• Newscale parameter inDotPlot
• Newkeep.sparse parameter inCreateGeneActivityMatrix`for a more memory efficient option
• Added ability to store model learned by UMAP and project newdata
• Newstrip.suffix option inRead10X.This changes the default behavior ofRead10X. A trailing-1 present in allcell names will not be removed by default.
• Addedgroup.by parameter toFeatureScatter

Changes

• Replace wilcox.test with limma implementation for a fasterFindMarkers default method
• Better point separation forVlnPlots when using thesplit.by option
• Efficiency improvements for anchor pairing
• Deprecate redundantsort.cell parameter inFeaturePlot
• Fixes to ensure correct class of Matrix passed to c++ functions
• Fixes for underscores in ident labels forDotPlot
• Ensure preservation of matrix dimnames inSampleUMI
• Fix non-standard evaluation problems insubset andWhichCells
• Default split violin option is now a multi group option
• Preserve alpha inFeaturePlot when usingblend
• Updateassay.used slot forDimReducs whenAssay is renamed

Seurat 3.1.4 (2020-02-20)

Changes

• Fixes toDoHeatmap to remain compatible with ggplot2v3.3
• Adoption ofpatchwork framework to replaceCombinePlots

Seurat 3.1.3 (2020-02-07)

Added

• New system agnosticWhich function to address problemswith FItSNE on Windows

Changes

• ExportCellsByIdentities andRowMergeSparseMatrices functions
• nCount and nFeature metadata variables retained after subset andupdated properly withUpdateSeuratObject
• Fix uwot support for running directly on feature matrices
• Fixes for keys with underscores
• Fix issue with leiden option forFindClusters
• 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 toRunCCA,RunTSNE,WhichCells,HTODemux,AddModuleScore,VlnPlot, andRidgePlot
• Enhancements for dealing withAssay-derivedobjects

Changed

• Only runCalcN (generates nFeatures and nCounts) whencounts changes
• Fix issue regarding colons in feature names
• Change object class testing to useinherits oris.* for R 4.0 compatability

Seurat 3.1.1 (2019-09-20)

Added

• NewRegroupIdents function to reassign idents based onmetadata column majority
• UpdateSymbolList function to pull new gene names fromHGNC
• Added support for H5AD layers as additional assays in aSeurat object

Changed

• Fix rownames issue when running UMAP on dist object
• Add support for new H5ADobsm andvarmstucture
• Fix issue when trying to read non-existent feature-level metadatafrom an H5AD file
• Fix in integration workflow when using SCTransform
• Improved error checking forAddModuleScore
• 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

• NewPrepSCTIntegration function to facilitateintegration afterSCTransform
• Reference-based integration with thereferenceparameter inFindIntegrationAnchors
• Reciprocal PCA as areduction option inFindIntegrationAnchors
• NewCollapseEmbeddingOutliers function
• EnableFindTransferAnchors afterSCTransform
• Added backColorDimSplit functionality
• Include a code of conduct
• Added uwot support as new default UMAP method
• AddedCheckDots to catch unused parameters and suggestupdated names
• Reductions andAssays assays functions tolist stored DimReducs and Assays

Changed

• Fix regex inLogSeuratCommand
• Check for NAs in feature names inRead10X
• Prevent dimnames for counts/data/scale.data matrices from beingarrays
• UpdatesReadH5AD 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
• EnableAssay specification inBuildClusterTree
• FixFeaturePlot when using bothblend andsplit.by
• Fix toWhichCells when passingcells andinvert
• Fix toHoverLocator labels and title
• Ensure features names don’t contain pipes (|)
• Deprecation ofRunLSI andRunALRA
• Fix legend bug when sorting inExIPlot

Seurat 3.0.2 (2019-06-07)

Added

• Flag to skip singleton grouping inFindClusters
• New custom colors for blendedFeaturePlots
• NewGetResidual function
• New Seurat/Monocle converters

Changed

• Fix issue where certain assays weren’t being shown in theSeurat object
• Fix issue where we weren’t updatingDimReduc objectcolumn names
• Fix line spacers inDoHeatmap
• Fix uninformative labels inFeaturePlot
• Fix unset identities when converting from SCE to Seurat
• Fix single colors being interpreted as palettes inSingleDimPlot
• Ensure factor levels are always numerically increasing afterFindClusters
• Better cell highlighting colors forDimPlot
• Fix tolevels<-.Seurat
• Add ability to use counts/scaled data inBuildClusterTree
• Minor fix to splitScaleData

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 withdifferent 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 inFindMarkers (#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 multimodaldata
• 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 objectsand the Seurat object
• Compatability updates for ggplot2 v2.3.0

Seurat 2.3.1 (2018-05-03)

Added

• Support forUMAPdimensional 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 changedto 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 wasremoved 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 wasremoved 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 AlignSubspaceextended 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 differentialexpression 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 andcc.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)