Merge pull request #19 from TrigosTeam/devel

Devel v1.3.1

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SPIAT
 Type: Package
 Title: Spatial Image Analysis of Tissues
-Version: 1.1.6
+Version: 1.3.1
 Authors@R: c(
     person(given = "Anna",
            family="Trigos",

NEWS.md

@@ -1,3 +1,11 @@
+# SPIAT 1.3.1
+
+* Added citation to the newly published paper.
+
+# SPIAT 1.3.0
+
+Development version on Bioconductor 3.18.
+
 # SPIAT 1.1.6
 
 BUG FIXES

README.md

@@ -30,5 +30,5 @@ The vignette with an overview of the package can be accessed from the top Menu u
 Yuzhou Feng, Tianpei Yang, Volkan Ozcoban, Mabel Li and John Zhu developed the package, including developing algorithms, writing code and designing the package. Yuzhou Feng and Maria Doyle did the package cleaning and wrote the tutorial. Anna Trigos conceived, supervised the work, developed algorithms and designed the package. 
 
 ## Paper reference
-Our latest paper is currently under review! However, you can have a look at our previous SPIAT pre-print here:
-https://www.biorxiv.org/content/10.1101/2020.05.28.122614v1
+Please check our latest paper for more information!
+Yuzhou Feng et al, Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments, Nature Communications (2023). DOI: 10.1038/s41467-023-37822-0

inst/CITATION

@@ -11,27 +11,37 @@ bibentry(
     person("Volkan", "Ozcoban"),
     person("Maria", "Doyle")
   ),
-  note = "R package version 1.1.6",
+  note = "R package version 1.3.1",
   year = "2023",
   url = "https://trigosteam.github.io/SPIAT/"),
 bibentry(
     bibtype = "article",
-    title = "SPIAT: An R package for the Spatial Image Analysis of Cells in Tissues",
+    title = "Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments",
     author =c(
+      person("Yuzhou", "Feng"),
       person("Tianpei", "Yang"),
+      person("John", "Zhu"),
+      person("Mabel", "Li"),
+      person("Maria", "Doyle"),
       person("Volkan", "Ozcoban"),
-      person("Anu", "Pasam"),
-      person("Nikolce", "Kocovski"),
+      person"Greg T", "Bass"),
       person("Angela", "Pizzolla"),
+      person("Lachlan", "Cain"),
+      person("Sirui", "Weng"),
+      person("Anupama", "Pasam"),
+      person("Nikolce", "Kocovski"),
       person("Yu-Kuan", "Huang"),
-      person("Greg", "Bass"),
       person("Simon P", "Keam"),
+      person("Terence P", "Speed"),
       person("Paul J", "Neeson"),
+      person("Richard B", "Pearson"),
       person("Shahneen K", "Sandhu"),
       person("David L", "Goode"),
       person("Anna S", "Trigos")
     ),
-    journal = "bioRxiv",
-    year = "2020",
-    doi = "10.1101/2020.05.28.122614"))
-
+    journal = "Nature Communications",
+    volume = "14",
+    number = "2697",
+    year = "2023",
+    doi = "10.1038/s41467-023-37822-0"))
+