NEWS

Seurat 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 4.4.0 (2023-09-28)

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)

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 (2022-11-07)

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 (2022-05-02)

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 (2021-10-17)

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 (2021-08-20)

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 (2021-05-20)

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 (2021-03-18)

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 (2021-01-29)

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 3.2.2 (2020-09-26)

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 (2020-09-07)

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 (2020-07-16)

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 (2020-04-16)

Added

New scale parameter in DotPlot
New keep.sparse parameter in CreateGeneActivityMatrix` 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 (2020-02-26)

Changes

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

Seurat 3.1.3 (2020-02-11)

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 (2019-12-12)

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 (2019-10-03)

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 (2019-06-14)

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 (2019-04-15)

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 (2018-07-17)

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 (2018-06-12)

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 (2018-05-05)

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 (2018-03-23)

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 (2017-08-22)

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

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)