Merge branch 'drieslab:suite_dev' into suite_dev

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 4.1.0
+Version: 4.1.1
 Authors@R: c(
 	person("Ruben", "Dries", email = "[email protected]",
 		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
@@ -27,11 +27,11 @@ URL: https://drieslab.github.io/Giotto/, https://github.com/drieslab/Giotto
 BugReports: https://github.com/drieslab/Giotto/issues
 RoxygenNote: 7.3.2
 Depends:
-    base (>= 4.1.0),
-    utils (>= 4.1.0),
-    R (>= 4.1.0),
+    base (>= 4.4.0),
+    utils (>= 4.4.0),
+    R (>= 4.4.0),
     methods,
-    GiottoClass (>= 0.3.2)
+    GiottoClass (>= 0.3.3)
 Imports:
     BiocParallel,
     BiocSingular,
@@ -60,7 +60,6 @@ Imports:
 Suggests:
     ArchR,
     arrow,
-    Biobase,
     biomaRt,
     ClusterR,
     clustree,
@@ -69,14 +68,12 @@ Suggests:
     DelayedMatrixStats,
     dendextend (>= 1.13.0),
     dplyr,
-    exactextractr,
     FactoMineR,
     factoextra,
     fitdistrplus,
     FNN,
     future,
     future.apply,
-    geometry,
     GiottoData,
     ggalluvial,
     ggdendro,
@@ -86,7 +83,6 @@ Suggests:
     graphcoloring,
     HDF5Array (>= 1.18.1),
     hdf5r,
-    htmlwidgets,
     jackstraw,
     kableExtra,
     knitr,
@@ -95,7 +91,6 @@ Suggests:
     multinet (>= 3.0.2),
     networkD3,
     pheatmap,
-    png,
     quadprog,
     harmony,
     R.utils,
@@ -105,10 +100,7 @@ Suggests:
     rhdf5,
     RTriangle (>= 1.6-0.10),
     Rvision,
-    S4Vectors,
     scater,
-    scatterpie,
-    scattermore,
     scran (>= 1.10.1),
     Seurat,
     sf,
@@ -121,15 +113,15 @@ Suggests:
     STexampleData,
     SummarizedExperiment,
     tidygraph,
-    tiff,
     trendsceek,
     testthat (>= 3.0.0),
-    qs
+    rmarkdown
 Remotes:
     drieslab/GiottoUtils,
     drieslab/GiottoClass,
     drieslab/GiottoVisuals
 Collate:
+    'ONTraC_wrapper.R'
     'auxiliary_giotto.R'
     'cell_segmentation.R'
     'clustering.R'