From 9079b9630efb54859a02ba176acf97d91873461f Mon Sep 17 00:00:00 2001 From: Janani Ravi Date: Fri, 24 Jul 2026 13:37:08 -0600 Subject: [PATCH] Add author and update citations/URLs Add Alexander McKim (with ORCID) to Authors@R in DESCRIPTION and update repository URL/BugReports to use JRaviLab capitalization. Replace the old package citation in README.Rmd and README.md with the new bioRxiv citation (DOI link) and note co-first authors. These changes keep author metadata and citation information current. --- DESCRIPTION | 8 +++++--- README.Rmd | 13 +++++++------ README.md | 12 ++++++++---- 3 files changed, 20 insertions(+), 13 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6c9a986..d741eb3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -9,7 +9,9 @@ Authors@R: c( person("Abhirupa", "Ghosh", , "abhirupa.ghosh@cuanschutz.edu", role = "ctb"), person("David", "Mayer", , "david.mayer@cuanschutz.edu", role = "ctb"), person("Evan", "Brenner", , "evan.brenner@cuanschutz.edu", role = "ctb"), - person("Charmie", "Vang", , "charmie.vang@cuanschutz.edu", role = "ctb") + person("Charmie", "Vang", , "charmie.vang@cuanschutz.edu", role = "ctb"), + person("Alexander", "McKim", , "alexander.mckim@cuanschutz.edu", role = "ctb", + comment = c(ORCID = "0000-0002-7802-7591")) ) Description: Interactive Shiny dashboard for exploring antimicrobial resistance (AMR) data and machine learning model results from the AMR package suite. @@ -58,6 +60,6 @@ biocViews: FunctionalGenomics, Genetics, Visualization -URL: https://github.com/jravilab/amRviz -BugReports: https://github.com/jravilab/amRviz/issues +URL: https://github.com/JRaviLab/amRviz +BugReports: https://github.com/JRaviLab/amRviz/issues Config/roxygen2/version: 8.0.0 diff --git a/README.Rmd b/README.Rmd index 605a8b5..a21c4d6 100644 --- a/README.Rmd +++ b/README.Rmd @@ -187,12 +187,13 @@ amRviz/ If you use `amRviz` in your research, please cite: -``` -Brenner E, Ghosh A, Boyer E, Vang C, Wolfe E, McKim A, Lesiyon R, Mayer D, Ravi J. (2026). -amR: an R package suite to predict antimicrobial resistance in bacterial pathogens. -R package version 0.99.0. -https://github.com/JRaviLab/amR -``` +> Ghosh A^, Brenner EP^, Boyer EA, McKim AP, Vang CK, Wolfe EP, Mayer D, Lesiyon RL, Ravi J. +> +> amR: an R package suite to predict antimicrobial resistance in bacterial pathogens. +> +> bioRxiv. 2026. DOI: [10.64898/2026.07.10.734579](https://doi.org/10.64898/2026.07.10.734579). + +^ Co-first authors ## For Bioconductor submission diff --git a/README.md b/README.md index 7094273..afa013e 100644 --- a/README.md +++ b/README.md @@ -197,10 +197,14 @@ organized into per-species subdirectories: If you use `amRviz` in your research, please cite: - Brenner E, Ghosh A, Boyer E, Vang C, Wolfe E, McKim A, Lesiyon R, Mayer D, Ravi J. (2026). - amR: an R package suite to predict antimicrobial resistance in bacterial pathogens. - R package version 0.99.0. - https://github.com/JRaviLab/amR +> Ghosh A^, Brenner EP^, Boyer EA, McKim AP, Vang CK, Wolfe EP, Mayer D, Lesiyon RL, Ravi J. +> +> amR: an R package suite to predict antimicrobial resistance in bacterial pathogens. +> +> bioRxiv. 2026. DOI: +> [10.64898/2026.07.10.734579](https://doi.org/10.64898/2026.07.10.734579). + +^ Co-first authors ## For Bioconductor submission