NEWS.md

Seurat 4.0.2 (2020-03-20)

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 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 (2020-02-20)

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)