diff --git a/DESCRIPTION b/DESCRIPTION index 784b8f4..995ba07 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -9,7 +9,9 @@ Authors@R: c( person("Charmie", "Vang", , "charmie.vang@cuanschutz.edu", role = "ctb"), person("Emily", "Boyer", , "emily.boyer@cuanschutz.edu", role = "ctb"), person("Raymond", "Lesiyon", , "raymond.lesiyon@cuanschutz.edu", role = "ctb"), - person("David", "Mayer", , "david.mayer@cuanschutz.edu", role = "ctb") + person("David", "Mayer", , "david.mayer@cuanschutz.edu", role = "ctb"), + person("Alexander", "McKim", , "alexander.mckim@cuanschutz.edu", role = "ctb", + comment = c(ORCID = "0000-0002-7802-7591")) ) Maintainer: Janani Ravi Description: amRdata starts with a user's species query and downloads all @@ -24,8 +26,8 @@ Encoding: UTF-8 Roxygen: list(markdown = TRUE) Depends: R (>= 4.5.0) -URL: https://github.com/JRaviLab/amR_data -BugReports: https://github.com/JRaviLab/amR_data/issues +URL: https://github.com/JRaviLab/amRdata +BugReports: https://github.com/JRaviLab/amRdata/issues Imports: arrow, BiocParallel, diff --git a/README.Rmd b/README.Rmd index daa9d62..0577afd 100644 --- a/README.Rmd +++ b/README.Rmd @@ -277,7 +277,7 @@ amRdata is designed to work seamlessly with other amR packages: ```r library(amRdata) library(amRml) -library(amRshiny) +library(amRviz) # 1. Curate data prepareGenomes("Shigella flexneri") @@ -294,17 +294,18 @@ launch_dashboard() - [amR](https://github.com/JRaviLab/amR): Suite metapackage - [amRml](https://github.com/JRaviLab/amRml): ML for AMR prediction -- [amRshiny](https://github.com/JRaviLab/amRshiny): Interactive dashboard +- [amRviz](https://github.com/JRaviLab/amRviz): Interactive dashboard ## Citation If you use `amRdata` in your research, please cite: -``` -Brenner E, Ghosh A, Wolfe E, Boyer E, Vang C, 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 ## Contributing diff --git a/README.md b/README.md index 268d529..acb3b3b 100644 --- a/README.md +++ b/README.md @@ -290,7 +290,7 @@ amRdata is designed to work seamlessly with other amR packages: ``` r library(amRdata) library(amRml) -library(amRshiny) +library(amRviz) # 1. Curate data prepareGenomes("Shigella flexneri") @@ -307,17 +307,22 @@ launch_dashboard() - [amR](https://github.com/JRaviLab/amR): Suite metapackage - [amRml](https://github.com/JRaviLab/amRml): ML for AMR prediction -- [amRshiny](https://github.com/JRaviLab/amRshiny): Interactive - dashboard +- [amRviz](https://github.com/JRaviLab/amRviz): Interactive dashboard ## Citation If you use `amRdata` in your research, please cite: - Brenner E, Ghosh A, Wolfe E, Boyer E, Vang C, 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 ## Contributing