Version 3.2.0

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

Additions

• 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).

Version 3.1.5

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

Additions:

• 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 stip.suffix option in Read10X
• Added group.by parameter to FeatureScatter

Version 3.1.4

Changes:

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

Version 3.1.3

Changes:

• Export CellsByIdentites and RowMergeSparseMatrices
• 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

Additions:

• New system-agnostic executable locator to fix FIt-SNE problem on Windows

Version 3.1.2

Changes:

• 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

Additions:

• 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

Version 3.1.1

Changes:

• 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

Additions:

• 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

Version 3.1.0

Changes:

• Bug fixes in LogSeuratCommand, Read10X, UpdateSeuratObject, FeaturePlot, WhichCells, and HoverLocator
• Prevent dimnames for counts/data/scale.data matrices from being arrays
• Updates ReadH5AD to distinguish FVF methods
• Sink all output from stdout to stderr
• Fix to scale.data cell ordering after subsetting
• Enable Assay specification in BuildClusterTree
• Ensure features names don't contain pipes (|)
• Deprecation of RunLSI and RunALRA
• Fix legend bug when sorting in ExIPlot

Additions:

• 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

Version 3.0.2

Changes:

• Improvements to visualization functions
• Improvements to identity assignment in FindClusters

Additions:

• New Seurat ↔ Monocle converters
• New GetResidual function
• Custom colors for blended FeaturePlot

Version 3.0.1

Changes:

• Improvements to conversion functions
• Fixes to various plotting functions
• Export new functions to the benefit of external packages

Additions:

• New global options using R's options manager
• New split.by parameter to ScaleData

Version 3.0.0

Changes:

• 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

Additions:

• 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