v1.1.5

DESCRIPTION

@@ -10,14 +10,14 @@ Description: BreastSubtypeR provides an assumption-aware, multi-method framework
     (iBreastSubtypeR) is included for interactive analyses and to support users
     without programming experience.
 Encoding: UTF-8
-Version: 1.1.5
+Version: 1.1.6
 biocViews: RNASeq, Software, GeneExpression, Classification, Preprocessing, Visualization
 Authors@R: c(
     person(given = "Qiao", family = "Yang", 
 	   role = c("aut", "cre"), 
            email="yq.kiuo@gmail.com", 
            comment = c(ORCID = "0000-0002-4098-3246")),
-    person(given = "Emmanouil", family = "Sifakis",
+    person(given = "Emmanouil G.", family = "Sifakis",
            role = c("aut"),
            email = "emmanouil.sifakis@ki.se",
            comment = c(ORCID = "0000-0001-9919-4471"))
@@ -53,7 +53,7 @@ Suggests:
     knitr,
     rmarkdown,
     testthat
-URL: https://doi.org/10.1093/nargab/lqaf131, https://github.com/yqkiuo/BreastSubtypeR
+URL: https://doi.org/10.18129/B9.bioc.BreastSubtypeR
 BugReports: https://github.com/yqkiuo/BreastSubtypeR/issues
 License: GPL-3
 VignetteBuilder: knitr

NEWS.md

@@ -1,4 +1,4 @@
-# BreastSubtypeR 1.1.5
+# BreastSubtypeR 1.1.6
 
 ## Highlights
 - Paper published in *NAR Genomics and Bioinformatics* (2025), **Editor’s Choice** (DOI: 10.1093/nargab/lqaf131).

README.md

@@ -20,18 +20,22 @@ It consolidates published intrinsic subtyping methods under one API and lets you
 
 **Plain text**
 
-Yang Q, Hartman J, Sifakis EG. BreastSubtypeR: a unified R/Bioconductor package for intrinsic molecular subtyping in breast cancer research. *NAR Genomics and Bioinformatics*. 2025. https://doi.org/10.1093/nargab/lqaf131
+Yang Q., Hartman J., Sifakis E.G. (2025). BreastSubtypeR: a unified R/Bioconductor package for intrinsic molecular subtyping in breast cancer research. *NAR Genomics and Bioinformatics*. <https://doi.org/10.1093/nargab/lqaf131>
 
 **BibTeX**
 ```bibtex
 @article{Yang2025BreastSubtypeR,
   author  = {Yang, Qiao and Hartman, Johan and Sifakis, Emmanouil G.},
-  title   = {BreastSubtypeR: a unified R/Bioconductor package for intrinsic molecular subtyping in breast cancer research},
+  title   = {{BreastSubtypeR}: a unified R/Bioconductor package for intrinsic molecular subtyping in breast cancer research},
   journal = {NAR Genomics and Bioinformatics},
   year    = {2025},
+  volume  = {7},
+  number  = {4},
+  pages   = {lqaf131},
   doi     = {10.1093/nargab/lqaf131},
   url     = {https://doi.org/10.1093/nargab/lqaf131}
 }
+
 ```
 </details>
 

inst/CITATION

@@ -1,41 +1,23 @@
 ## inst/CITATION
 
-pkg <- utils::packageDescription("BreastSubtypeR")
-pkgVersion <- pkg$Version
-pkgYear <- if (!is.null(pkg$Date)) substr(pkg$Date, 1, 4) else format(Sys.Date(), "%Y")
+citHeader("To cite BreastSubtypeR, please use the following references.")
 
-citHeader("To cite BreastSubtypeR, please use the following references.\n")
-
-# Journal article
 paper <- bibentry(
   bibtype = "Article",
-  author = c(
+  title   = "BreastSubtypeR: a unified R/Bioconductor package for intrinsic molecular subtyping in breast cancer research",
+  author  = c(
     person(given = "Qiao",  family = "Yang"),
     person(given = "Johan", family = "Hartman"),
-    person(given = "Emmanouil", family = "Sifakis")
+    person(given = "Emmanouil G.", family = "Sifakis")
   ),
-  title   = "BreastSubtypeR: A Unified R/Bioconductor Package for Intrinsic Molecular Subtyping in Breast Cancer Research",
   journal = "NAR Genomics and Bioinformatics",
   year    = "2025",
-  note    = "Editor's Choice",
+  volume  = "7",
+  number  = "4",
+  pages   = "lqaf131",
   doi     = "10.1093/nargab/lqaf131",
-  url     = "https://doi.org/10.1093/nargab/lqaf131",
-  textVersion =
-    "Yang Q., Hartman J., Sifakis E.G. BreastSubtypeR: A Unified R/Bioconductor Package for Intrinsic Molecular Subtyping in Breast Cancer Research. NAR Genomics and Bioinformatics. 2025. https://doi.org/10.1093/nargab/lqaf131"
+  url     = "https://doi.org/10.1093/nargab/lqaf131"
 )
 
-# Package manual
-pkgCite <- bibentry(
-  bibtype = "Manual",
-  title   = sprintf("BreastSubtypeR: R package version %s", pkgVersion),
-  author  = c(
-    person(given = "Qiao",      family = "Yang"),
-    person(given = "Emmanouil", family = "Sifakis")
-  ),
-  year    = pkgYear,
-  url     = "https://github.com/yqkiuo/BreastSubtypeR"
-)
-
-citFooter("\nPlease also cite R itself and the packages on which BreastSubtypeR depends.")
-
-invisible()  # <-- do NOT return c(paper, pkgCite)
+## Auto-generate the “Manual” entry from DESCRIPTION
+pkg_manual <- citation(auto = meta)

vignettes/BreastSubtypeR.Rmd

@@ -44,7 +44,7 @@ BiocManager::install("BreastSubtypeR")
 
 If you use **BreastSubtypeR**, please cite:
 
-- Yang Q., Hartman J., Sifakis E.G. (2025). *BreastSubtypeR: A Unified R/Bioconductor Package for Intrinsic Molecular Subtyping in Breast Cancer Research*. **NAR Genomics and Bioinformatics**. <https://doi.org/10.1093/nargab/lqaf131>
+- Yang Q., Hartman J., Sifakis E.G. (2025). *BreastSubtypeR: a unified R/Bioconductor package for intrinsic molecular subtyping in breast cancer research*. **NAR Genomics and Bioinformatics**, 7(4):131. <https://doi.org/10.1093/nargab/lqaf131>
 
 For BibTeX/LaTeX, run in R:
 
@@ -239,7 +239,7 @@ clinical validation requires paired clinical assay data.\
 
 ## References
 
-- Yang Q., Hartman J., Sifakis E.G. (2025). BreastSubtypeR: A Unified R/Bioconductor Package for Intrinsic Molecular Subtyping in Breast Cancer Research. *NAR Genomics and Bioinformatics*. <https://doi.org/10.1093/nargab/lqaf131>
+- Yang Q., Hartman J., Sifakis E.G. (2025). BreastSubtypeR: a unified R/Bioconductor package for intrinsic molecular subtyping in breast cancer research. *NAR Genomics and Bioinformatics*, 7(4):131. <https://doi.org/10.1093/nargab/lqaf131>
 
 -  Parker JS, Mullins M, Cheang MCU, Leung S, Voduc D, Vickery T, *et al.* (2009). Supervised risk predictor of breast cancer based on intrinsic subtypes. *J Clin Oncol*, 27(8):1160–1167. <https://doi.org/10.1200/JCO.2008.18.1370>