updated with paper citation

BodenmillerGroup · Jan 4, 2024 · 0096758 · 0096758
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: cytoviewer
-Version: 1.3.0
+Version: 1.3.1
 Title: An interactive multi-channel image viewer for R
 Description: 
     This R package supports interactive visualization of multi-channel images 

diff --git a/NEWS b/NEWS
@@ -39,3 +39,6 @@ Changes in version 1.1.2 (2023-10-09):
 
 Changes in version 1.1.3 (2023-10-19): 
 + enlarged default display area and changed default color settings
+
+Changes in version 1.3.1 (2024-01-04): 
++ updated README and added citation file
diff --git a/README.md b/README.md
@@ -20,7 +20,9 @@ Channels) and cell-level visualization (Masks). It allows users
 to overlay individual images with segmentation masks, integrates well 
 with [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) / [SpatialExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) 
 and [CytoImageList](https://www.bioconductor.org/packages/release/bioc/html/cytomapper.html)
-objects for metadata and image visualization and supports image downloads.
+objects for metadata and image visualization and supports image downloads.  
+
+Read the **BMC Bioinformatics paper** here: [doi.org/10.1186/s12859-023-05546-z](doi.org/10.1186/s12859-023-05546-z)
 
 ## Check status
 
@@ -102,11 +104,11 @@ issue a pull request.
 
 ## Citation
 
-If you are using `cytoviewer` in your work, please cite the released preprint as:
+If you are using `cytoviewer` in your work, please cite the paper as:
 
 ```
-Lasse Meyer, Nils Eling, and Bernd Bodenmiller (2023). cytoviewer: an R/Bioconductor package for interactive 
-visualization and exploration of highly multiplexed imaging data, biorxiv, doi.org/10.1101/2023.05.24.542115
+Meyer, L., Eling, N., & Bodenmiller, B. (2024). cytoviewer: an R/Bioconductor package for interactive visualization 
+and exploration of highly multiplexed imaging data. BMC Bioinformatics, doi.org/10.1186/s12859-023-05546-z
 ```
 
 

diff --git a/inst/CITATION b/inst/CITATION
@@ -0,0 +1,12 @@
+
+citHeader("To cite the package 'cytoviewer' in publications use:")
+
+citEntry(entry="article",
+         title = "cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data",
+         author = personList(as.person("Lasse Meyer"),
+                             as.person("Nils Eling"),
+                             as.person("Bernd Bodenmiller")),
+         year = 2024,
+         journal = "BMC Bioinformatics",
+	 doi = "doi.org/10.1186/s12859-023-05546-z",
+         textVersion = "Lasse Meyer, Nils Eling, Bernd Bodenmiller (2024). cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data. BMC Bioinformatics, doi: doi.org/10.1186/s12859-023-05546-z")