Version 3.2.2

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

Version 3.2.1

Deprecations

• 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

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

Additions

• 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

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