Merge pull request #541 from satijalab/release/4.0.1

Prep for CRAN release of 4.0.1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.0.0.9015
-Date: 2021-03-15
+Version: 4.0.1
+Date: 2021-03-17
 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>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
 Authors@R: c(

NEWS.md

@@ -1,5 +1,4 @@
-# Seurat develop
-
+# Seurat 4.0.1 (2020-03-17)
 ## Added
 - Add direction option to `PlotClusterTree()`
 - Add `cols` parameter to `JackStrawPlot()`

R/preprocessing.R

@@ -1057,7 +1057,10 @@ Read10X_Image <- function(image.dir, filter.matrix = TRUE, ...) {
 #' \dontrun{
 #' # For local files:
 #'
-#' expression_matrix <- ReadMtx(genes="count_matrix.mtx.gz", features="features.tsv.gz", cells="barcodes.tsv.gz")
+#' expression_matrix <- ReadMtx(
+#'   mtx = "count_matrix.mtx.gz", features = "features.tsv.gz",
+#'   cells = "barcodes.tsv.gz"
+#' )
 #' seurat_object <- CreateSeuratObject(counts = expression_matrix)
 #'
 #' # For remote files:

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://travis-ci.com/satijalab/seurat.svg?branch=master)](https://travis-ci.com/satijalab/seurat)
+[![Build Status](https://travis-ci.com/satijalab/seurat.svg?branch=master)](https://travis-ci.com/github/satijalab/seurat)
 [![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/satijalab/seurat?branch=master&svg=true)](https://ci.appveyor.com/project/satijalab/seurat)
 [![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)

cran-comments.md

@@ -1,7 +1,6 @@
-# Seurat v4.0.0
+# Seurat v4.0.1
 
 ## Test environments
-* local Ubuntu 16.04.6 install, R 4.0.3
 * local Ubuntu 18.04.4 install, R 4.0.3
 * local Ubuntu 20.04 install, R 4.0.3
 * local Windows 10 install, R 4.0.3
@@ -15,8 +14,8 @@ There were no ERRORs, WARNINGs, or NOTEs
 
 ## Downstream dependencies
 
-There is one package that depends on Seurat: tidyseurat; this update does not impact its functionality
+There are no packages that depend on Seurat.
 
-There are three packages that imports Seurat: scMappR, Signac, and SoupX; this update does not impact their functionality
+There are six packages that imports Seurat: CDSeq, DUBStepR, scMappR, Signac, SignacX, and SoupX; this update does not impact their functionality
 
-There are ten packages that suggest Seurat: BisqueRNA, clustree, DIscBIO, nanny, rliger, Rmagic, scSorter, singleCellHaystack, treefit, VAM; this update does not impact their functionality.
+There are eleven packages that suggest Seurat: BisqueRNA, clustree, conos, DIscBIO, dyngen, nanny, rliger, Rmagic, singleCellHaystack, treefit, VAM; this update does not impact their functionality.