diff --git a/DESCRIPTION b/DESCRIPTION index 7956cdb..d2caa47 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: amRml -Title: Machile learning framework to predict AMR across molecular scales | pkg 2 of 3-pkg amR suite +Title: Machine learning framework to predict AMR across molecular scales | pkg 2 of 3-pkg amR suite Version: 0.99.0 Authors@R: c( person("Janani", "Ravi", , "janani.ravi@cuanschutz.edu", role = c("aut", "cre"), @@ -7,7 +7,11 @@ Authors@R: c( person("Ethan", "Wolfe", , "ethan.wolfe@cuanschutz.edu", role = "ctb"), person("Evan", "Brenner", , "evan.brenner@cuanschutz.edu", role = "ctb"), person("Abhirupa", "Ghosh", , "abhirupa.ghosh@cuanschutz.edu", role = "ctb"), - person("David", "Mayer", , "david.mayer@cuanschutz.edu", role = "ctb") + person("David", "Mayer", , "david.mayer@cuanschutz.edu", role = "ctb"), + person("Emily", "Boyer", , "emily.boyer@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: Comprehensive machine learning (ML) pipeline for predicting antimicrobial resistance (AMR) in ESKAPE pathogens across molecular scales (gene, protein, @@ -16,7 +20,7 @@ Description: Comprehensive machine learning (ML) pipeline for predicting antimic (geographic, temporal, species). Includes model evaluation, feature importance analysis, cross-scale performance comparison, and functional characterization of top features. Designed to work with data from amRdata package and generate - results for amRshiny visualization. Can work independently with example + results for amRviz visualization. Can work independently with example ESKAPE pathogen datasets, too. License: BSD_3_clause + file LICENSE Encoding: UTF-8 diff --git a/README.Rmd b/README.Rmd index 68a00f0..7502209 100644 --- a/README.Rmd +++ b/README.Rmd @@ -115,7 +115,7 @@ amRml is designed to work seamlessly with other amR packages: ```r library(amRdata) library(amRml) -library(amRshiny) +library(amRviz) # 1. Curate data prepareGenomes("Shigella flexneri") @@ -130,18 +130,19 @@ launchAMRDashboard() ## Related packages - [amR](https://github.com/JRaviLab/amR): Suite metapackage -- [amRdata](https://github.com/JRaviLab/amRml): Data preparation for AMR prediction -- [amRshiny](https://github.com/JRaviLab/amRshiny): Interactive dashboard +- [amRdata](https://github.com/JRaviLab/amRdata): Data preparation for AMR prediction +- [amRviz](https://github.com/JRaviLab/amRviz): Interactive dashboard ## Citation If you use `amRml` 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 3940387..6e30ffc 100644 --- a/README.md +++ b/README.md @@ -144,7 +144,7 @@ amRml is designed to work seamlessly with other amR packages: ``` r library(amRdata) library(amRml) -library(amRshiny) +library(amRviz) # 1. Curate data prepareGenomes("Shigella flexneri") @@ -160,19 +160,24 @@ launchAMRDashboard() ## Related packages - [amR](https://github.com/JRaviLab/amR): Suite metapackage -- [amRdata](https://github.com/JRaviLab/amRml): Data preparation for AMR - prediction -- [amRshiny](https://github.com/JRaviLab/amRshiny): Interactive - dashboard +- [amRdata](https://github.com/JRaviLab/amRdata): Data preparation for + AMR prediction +- [amRviz](https://github.com/JRaviLab/amRviz): Interactive dashboard ## Citation If you use `amRml` 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