Merge pull request #234 from satijalab/release/3.1.2

Prep for CRAN release of 3.1.2

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 3.1.1.9024
-Date: 2019-12-11
+Version: 3.1.2
+Date: 2019-12-12
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details.
 Authors@R: c(
@@ -62,7 +62,7 @@ Imports:
     tools,
     tsne,
     utils,
-    uwot
+    uwot (>= 0.1.5)
 LinkingTo: Rcpp (>= 0.11.0), RcppEigen, RcppProgress
 License: GPL-3 | file LICENSE
 LazyData: true
@@ -81,8 +81,9 @@ Collate:
     'tree.R'
     'utilities.R'
     'zzz.R'
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
 Encoding: UTF-8
+biocViews:
 Suggests:
     loomR,
     testthat,

NAMESPACE

@@ -182,6 +182,7 @@ export(CellCycleScoring)
 export(CellScatter)
 export(CellSelector)
 export(Cells)
+export(CellsByIdentities)
 export(CollapseEmbeddingOutliers)
 export(CollapseSpeciesExpressionMatrix)
 export(ColorDimSplit)
@@ -273,6 +274,7 @@ export(ReadH5AD)
 export(Reductions)
 export(RegroupIdents)
 export(RelativeCounts)
+export(RenameAssays)
 export(RenameCells)
 export(RenameIdents)
 export(ReorderIdent)

NEWS.md

@@ -3,6 +3,17 @@ 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/)
 
 
+## [3.1.2] - 2019-12-11
+### Added
+- New silent slot updater
+- New random seed options to `RunCCA`, `RunTSNE`, `WhichCells`, `HTODemux`, `AddModuleScore`, `VlnPlot`, and `RidgePlot`
+- Enhancements for dealing with `Assay`-derived objects
+
+### Changed
+- Only run `CalcN` (generates nFeatures and nCounts) when `counts` changes
+- Fix issue regarding colons in feature names
+- Change object class testing to use `inherits` or `is.*` for R 4.0 compatability
+
 ## [3.1.1] - 2019-09-20
 ### Added
 - New `RegroupIdents` function to reassign idents based on metadata column majority

R/utilities.R

@@ -432,7 +432,7 @@ CellCycleScoring <- function(
   set.ident = FALSE,
   ...
 ) {
-  name <- 'Cell Cycle'
+  name <- 'Cell.Cycle'
   features <- list('S.Score' = s.features, 'G2M.Score' = g2m.features)
   object.cc <- AddModuleScore(
     object = object,

README.md

@@ -3,7 +3,7 @@
 [![CRAN Version](https://www.r-pkg.org/badges/version/Seurat)](https://cran.r-project.org/package=Seurat)
 [![CRAN Downloads](https://cranlogs.r-pkg.org/badges/Seurat)](https://cran.r-project.org/package=Seurat)
 
-# Seurat v3.1.1
+# Seurat v3.1.2
 
 
 Seurat is an R toolkit for single cell genomics, developed and maintained by the Satija Lab at NYGC.

cran-comments.md

@@ -1,11 +1,11 @@
-# Seurat v3.1.1
+# Seurat v3.1.2
 
 ## Test environments
-* local Ubuntu 16.04.6 and 18.04.2 installs, R 3.5.3
+* local Ubuntu 16.04.6 and 18.04.2 installs, R 3.6.1
 * Ubuntu 16.04.6 (on travis-ci), R 3.6.1
 * macOS 10.13.3 (on travis-ci), R 3.6.1
 * Windows Server 2012 R2 (on AppVeyor), R 3.6.1 Patched
-* win-builder (oldrelease, release, devel)
+* win-builder (oldrelease, release, devel, devel_gcc8)
 
 ## R CMD check results
 There were no ERRORs or WARNINGs
@@ -33,4 +33,6 @@ There were 3 NOTEs:
 
 ## Downstream dependencies
 
-There are three packages that suggest Seurat: BisqueRNA, clustreen, and iCellR; this update does not impact their functionality.
+There is one pacakge that imports Seurat: multicross; this update does not impact its functionality
+
+There are five packages that suggest Seurat: BisqueRNA, clustree, diem, iCellR, and Rmagic; this update does not impact their functionality.