Merge pull request #3268 from satijalab/develop

Seurat v3.2.0

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: Seurat
-Version: 3.1.5
-Date: 2020-04-14
+Version: 3.2.0
+Date: 2020-07-15
 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 Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details. Please note:  SDMTools is available is available from the CRAN archives with install.packages(<"https://cran.rstudio.com//src/contrib/Archive/SDMTools/SDMTools_1.1-221.2.tar.gz">, repos = NULL); it is not in the standard repositories.
+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 Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details.
 Authors@R: c(
   person(given = 'Rahul', family = 'Satija', email = 'rsatija@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0001-9448-8833')),
   person(given = 'Andrew', family = 'Butler', email = 'abutler@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0003-3608-0463')),
@@ -37,14 +37,16 @@ Imports:
     ica,
     igraph,
     irlba,
+    jsonlite,
     KernSmooth,
     leiden (>= 0.3.1),
     lmtest,
     MASS,
     Matrix (>= 1.2-14),
+    miniUI,
     patchwork,
     pbapply,
-    plotly,
+    plotly (>= 4.9.0),
     png,
     RANN,
     RColorBrewer,
@@ -57,9 +59,11 @@ Imports:
     Rtsne,
     scales,
     sctransform (>= 0.2.0),
+    shiny,
+    spatstat,
     stats,
+    tibble,
     tools,
-    tsne,
     utils,
     uwot (>= 0.1.5)
 LinkingTo: Rcpp (>= 0.11.0), RcppEigen, RcppProgress
@@ -80,12 +84,10 @@ Collate:
     'tree.R'
     'utilities.R'
     'zzz.R'
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 Encoding: UTF-8
-biocViews:
 Suggests:
     loomR,
-    SDMTools,
     testthat,
     hdf5r,
     S4Vectors,
@@ -98,6 +100,7 @@ Suggests:
     GenomeInfoDb,
     IRanges,
     rtracklayer,
+    Rfast2,
     monocle,
     Biobase,
     VGAM,