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