# News
All notable changes to Seurat will be documented in this file.
The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)

## [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)