diff --git a/DESCRIPTION b/DESCRIPTION index ed0c668..90ed6d4 100755 --- a/DESCRIPTION +++ b/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 diff --git a/NEWS.md b/NEWS.md index a6a97e4..509192b 100755 --- a/NEWS.md +++ b/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). diff --git a/README.md b/README.md index e4f703e..7e6d791 100755 --- a/README.md +++ b/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*. **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} } + ``` diff --git a/inst/CITATION b/inst/CITATION index 0b69e59..573ff1f 100644 --- a/inst/CITATION +++ b/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) \ No newline at end of file diff --git a/man/BreastSubtypeR.Rd b/man/BreastSubtypeR.Rd index 59c03ad..057f6d7 100755 --- a/man/BreastSubtypeR.Rd +++ b/man/BreastSubtypeR.Rd @@ -57,7 +57,7 @@ methods; FPKM for SSP-based methods. Authors: \itemize{ - \item Emmanouil Sifakis \email{emmanouil.sifakis@ki.se} (\href{https://orcid.org/0000-0001-9919-4471}{ORCID}) + \item Emmanouil G. Sifakis \email{emmanouil.sifakis@ki.se} (\href{https://orcid.org/0000-0001-9919-4471}{ORCID}) } } diff --git a/vignettes/BreastSubtypeR.Rmd b/vignettes/BreastSubtypeR.Rmd index 62da02d..6cdb19f 100755 --- a/vignettes/BreastSubtypeR.Rmd +++ b/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**. +- 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. 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*. +- 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. - 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.