NEWS.md

In gcday/seurat_fresh: Tools for Single Cell Genomics

News

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

[3.0.2] - 2019-06-07

Added

• Flag to skip singleton grouping in FindClusters
• New custom colors for blended FeaturePlots
• New GetResidual function
• New Seurat/Monocle converters

Changed

• Fix issue where certain assays weren't being shown in the Seurat object
• Fix issue where we weren't updating DimReduc object column names
• Fix line spacers in DoHeatmap
• Fix uninformative labels in FeaturePlot
• Fix unset identities when converting from SCE to Seurat
• Fix single colors being interpreted as palettes in SingleDimPlot
• Ensure factor levels are always numerically increasing after FindClusters
• Better cell highlighting colors for DimPlot
• Fix to levels<-.Seurat
• Add ability to use counts/scaled data in BuildClusterTree
• Minor fix to split ScaleData

[3.0.1] - 2019-05-16

Added

• Add global option (Seurat.memsafe) to skip gc() calls
• Restore draw.lines to DoHeatmap, maintain size of color bar with different number of features (#1429)
• Enable split.by parameter for ScaleData
• Add slot parameter to FeaturePlot (#1483)
• Add assay parameter to DotPlot (#1404)

Changed

• Fix to color options for VlnPlot with split.by option (#1425)
• Improvements to conversion functions (loom, SCE)
• Fix for cluster tree reordering (#1434)
• Fix PercentageFeatureSet for single feature case
• Fix to fold change calculation and filtering for other slots in FindMarkers (#1454)
• Keep title vectorized in AugmentPlot (#1515)
• Export LogSeuratCommand function
• Fix for FindConservedMarkers when one ident is missing from a group (#1517)

[3.0.0] - 2019-04-16

Added

• 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

Changed

• 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

[2.3.4] - 2018-07-13

Added

• GetIdent function added to pull identity info

Changed

• DiffusionMap dependency replaced with destiny to avoid archival
• Java dependency removed and functionality rewritten in Rcpp
• Speed and efficiency improvements for Rcpp code
• More robust duplicate handling in CellCycleScoring

[2.3.3] - 2018-07-02

Added

• New HTOHeatmap function
• Support for custom PNG arguments for vector-friendly plotting
• Fix for 'NA'-labeled cells disappearing with custom color scale

Changed

• Replaced FNN with RANN
• Removed unused compiler flags
• Moved several lightly-used packages from 'imports' to 'suggests'

[2.3.2] - 2018-06-11

Added

• RenameCells added for easy renaming of all cells
• Read10X_h5 added to read in 10X formatted h5 files
• SetAssayData ensures cell order is the same between assay objects and the Seurat object
• Compatability updates for ggplot2 v2.3.0

[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)

gcday/seurat_fresh documentation built on June 23, 2019, 12:02 a.m.