News

All notable changes to Seurat will be documented in this file. The format is based on Keep a Changelog

[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

[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

[3.1.4] - 2020-02-20

Changes

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

[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

[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

[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

[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

[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

[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)

[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

[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

[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’

[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

[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.

[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)

[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)

[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

[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

[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

[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)