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

Version 2.3.3

Changes:

• New HTOHeatmap function
• Removed unused compiler flags
• Support for custom PNG arguments for vector-friendly plotting
• Fix for 'NA'-labeled cells disappearing with custom color scales
• Moved several lightly-used packages from 'imports' to 'suggests'

Version 2.3.2

• New functions for reading in and manipulating data
• Better support for and validation of assay data
• Compatability updates for ggplot2 v2.3.0

Version 2.3.1

Changes:

• Support for UMAP dimensional reduction technique
• New conversion functions
• Dependency update: requires R 3.4.0 or higher and Matrix 1.2-14 or higher
• Bug fixes, including memory enhancements to FetchData and AddModuleScore, as well as improvments to visualization functions

Version 2.3.0

Changes:

• 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
• MetaDE replaced with metap for combining p-values (MetaDE was removed from CRAN)
• NMF heatmaps replaced (NMF to be archived by CRAN)

Version 2.2.1

Changes:

• Support for multiple-dataset alignment with RunMultiCCA and AlignSubspace
• New methods for evaluating alignment performance
• MetaDE replaced with metap for combining p-values (MetaDE was removed from CRAN)
• NMF heatmaps replaced (NMF to be archived by CRAN)

Version 2.1.0

Version 2.1
Changes:

• Support for using MAST and DESeq2 packages for differential expression testing in FindMarkers
• Support for multi-modal single-cell data via @assay slot

Version 2.0.1

Version 2.0.1 -- CRAN Release

Seurat is now available on CRAN. This version on Seurat is compatible with 2.0.0, but includes updated documentation, example data sets, and minor bug fixes. Installation can now be done with install.packages(). Binaries are no longer provided as they are built by CRAN. See the CRAN package page for Seurat here.

Version 2.0.0

Version 2.0
Changes:

• Preprint released for integrated analysis of scRNA-seq across conditions, technologies and species
• Significant restructuring of code to support clarity and dataset exploration
• Methods for scoring gene expression and cell-cycle phase