merge

Merge remote-tracking branch 'upstream/suite' into suite

# Conflicts:
#	R/convenience_visiumHD.R

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 4.1.4
+Version: 4.1.5
 Authors@R: c(
 	person("Ruben", "Dries", email = "[email protected]",
 		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
@@ -28,7 +28,7 @@ RoxygenNote: 7.3.2
 Depends:
     R (>= 4.4.1),
     methods,
-    GiottoClass (>= 0.3.3)
+    GiottoClass (>= 0.4.1)
 Imports:
     BiocParallel,
     BiocSingular,
@@ -37,8 +37,8 @@ Imports:
     dbscan (>= 1.1-3),
     ggraph,
     ggplot2 (>= 3.1.1),
-    GiottoUtils (>= 0.1.12),
-    GiottoVisuals (>= 0.2.5),
+    GiottoUtils (>= 0.2.0),
+    GiottoVisuals (>= 0.2.6),
     igraph (>= 1.2.4.1),
     Matrix (>= 1.6-2),
     MatrixGenerics,

NEWS.md

@@ -1,4 +1,23 @@
 
+# Giotto 4.1.5 (2024/11/08)
+
+## Enhancements
+* `createGiottoXeniumObject()` auto loading for morphology focus images, image directory loading, auto centroid calculation, allow skipping transcript loading
+
+## Website changes
+* New Analysis mini tutorials for showing common processing functions independently of the spatial technology.
+* New Slide-seq and OpenST examples.
+* New Contributing tab with guidelines for contributing to the package and the website.
+* New Visualizations tutorials.
+* New Giotto workflow and Core Functions tutorials under Get Started tab.
+* New Create and change Giotto instructions tutorial.
+* New Spatial Patterns tutorials section.
+* New tutorials under Interactivity for regions selection with vitessceR.
+* New Multi-samples tutorials section.
+* Updated technologies examples.
+* Updated tutorials for using Docker and Singularity Giotto containers.
+* Homogenized variable names across examples and tutorials.
+
 # Giotto 4.1.4 (2024/10/30)
 
 ## Changes