News

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

[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)