Update news, bump version

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
 Version: 4.4.0
-Date: 2023-09-15
+Date: 2023-09-26
 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(
@@ -58,6 +58,7 @@ Imports:
     plotly (>= 4.9.0),
     png,
     progressr,
+    purrr,
     RANN,
     RColorBrewer,
     Rcpp (>= 1.0.7),
@@ -67,9 +68,9 @@ Imports:
     ROCR,
     Rtsne,
     scales,
-    scattermore (>= 0.7),
-    sctransform (>= 0.3.5),
-    SeuratObject (>= 4.1.3),
+    scattermore (>= 1.2),
+    sctransform (>= 0.4.0),
+    SeuratObject (>= 4.1.4),
     shiny,
     spatstat.explore,
     spatstat.geom,

NEWS.md

@@ -1,4 +1,4 @@
-# Seurat 4.4.0 (2023-09-15)
+# Seurat 4.4.0 (2023-09-27)
 
 ## Added
 - Added parallelization support with speed improvements for `PrepSCTFindMarkers` 
@@ -7,11 +7,12 @@
 ## Changes
 - Fix bug in `as.Seurat.SingleCellExperiment()` ([#6692](https://github.com/satijalab/seurat/issues/6692))
 - Support for Visium probe information introduced in Spaceranger 2.1 ([#7141](https://github.com/satijalab/seurat/pull/7141))
-- Add `LoadCurioSeeker` to load sequencing-based spatial datasets generated using the Curio Seeker ([#744](https://github.com/satijalab/seurat-private/pull/744))
-- Fix fold change calculation for assays ([#739](https://github.com/satijalab/seurat-private/pull/739))
+- Add `LoadCurioSeeker` to load sequencing-based spatial datasets generated using the Curio Seeker 
+- Fix fold change calculation for assays ([#7095](https://github.com/satijalab/seurat/issues/7095))
 - Fix `pt.size` bug when rasterization is set to true ([#7379](https://github.com/satijalab/seurat/issues/7379)) 
 - Fix `FoldChange` and `FindMarkers` to support all normalization approaches ([#7115](https://github.com/satijalab/seurat/pull/7115),[#7110](https://github.com/satijalab/seurat/issues/7110),[#7095](https://github.com/satijalab/seurat/issues/7095),[#6976](https://github.com/satijalab/seurat/issues/6976),[#6654](https://github.com/satijalab/seurat/issues/6654),[#6701](https://github.com/satijalab/seurat/issues/6701),[#6773](https://github.com/satijalab/seurat/issues/6773), [#7107](https://github.com/satijalab/seurat/issues/7107))
 - Fix for handling newer ParseBio formats in `ReadParseBio` ([#7565](https://github.com/satijalab/seurat/pull/7565))
+- Fix for handling rasterization by default ([#7842](https://github.com/satijalab/seurat/pull/7842))
 
 # Seurat 4.3.0 (2022-11-18)
 

cran-comments.md

@@ -1,30 +1,16 @@
-# Seurat v4.2.1
+# Seurat v4.4.0
 
 ## Test environments
-* local Ubuntu 20.04 install, R 4.1.3
+* local Ubuntu 20.04 install, R 4.3.1
 * win-builder (release, devel)
 
 ## R CMD check results
-There were no ERRORs or WARNINGs
-
-There was one NOTE:
-
-* checking CRAN incoming feasibility ... NOTE
-Maintainer: 'Paul Hoffman <seurat@nygenome.org>'
-
-Found the following (possibly) invalid URLs:
-  URL: https://www.science.org/doi/abs/10.1126/science.aad0501
-    From: man/cc.genes.Rd
-          man/cc.genes.updated.2019.Rd
-    Status: 503
-    Message: Service Unavailable
-
-This URL is valid and the service still exists. When navigating to the URL either via the documentation or directly, you are taken to the correct article
+There were no ERRORs or WARNINGs.
 
 ## Downstream dependencies
 
 There no packages that depend on Seurat
 
-There are sixteen packages that import Seurat: CAMML, CIDER, DR.SC, DUBStepR, maple, Platypus, rPanglaoDB, scDiffCom, scMappR, SCRIP, scRNAstat, Signac, SignacX, SoupX, spruce, and tidyseurat; this update does not impact their functionality
+There are forty-five packages that import Seurat: AnanseSeurat, APL, bbknnR, benchdamic, CAMML, CIDER, COTAN, CSCDRNA, Dino, DR.SC, DWLS, ggsector, gsdensity, infercnv, IRISFGM, mixhvg, Nebulosa, pipeComp, PRECAST, ProFAST, rPanglaoDB, scAnnotate, scBFA, scBubbletree, scCB2, scDataviz, scDiffCom, scFeatures, scGate, scMappR, scperturbR, scpoisson, SCRIP, scRNAseqApp, scRNAstat, scTreeViz, SignacX, singleCellTK, SoupX, Spaniel, SPECK, speckle, SpotClean, stJoincount, and STREAK; this update does not impact their functionality
 
-There are twelve packages that suggest Seurat: BisqueRNA, CIARA, ClustAssess, clustree, conos, DIscBIO, dyngen, harmony, rliger, Rmagic, treefit, and VAM; this update does not impact their functionality.
+There are fifty-one packages that suggest Seurat: ASURAT, BayesSpace, BisqueRNA, Canek, cellpypes, CIARA, ClustAssess, clustifyr, clustifyrdatahub, clustree, combiroc, conos, countland, CRMetrics, decoupleR, DIscBIO, dittoSeq, dorothea, dyngen, EasyCellType, EpiMix, escape, fcoex, FEAST, fgsea, GeomxTools, grandR, harmony, M3Drop, MOFA2, monocle, muscData, progeny, RESET, rliger, SCORPIUS, SCpubr, scRepertoire, scTensor, Signac, SimBenchData, SimBu, spatialHeatmap, SPOTlight, TAPseq, TCGAbiolinks, tidybulk, treefit, tricycle, UCell, and VAM; this update does not impact their functionality.