AMRgenConverter

A Shiny app for importing antibiogram data with AMRgen::import_pheno(), summarising it with AMRgen::summarise_pheno(), and exporting NCBI or EBI-ready outputs.

Features

• Upload CSV, TSV, TXT, compressed AST input files, or Excel workbooks (.xls/.xlsx)
• Import supported source formats including NCBI, EBI, WHONET, Vitek, MicroScan, Phoenix, and Sensititre
• Optionally interpret AST values with EUCAST, CLSI, or ECOFF rules during import
• Review imported long-format phenotype data in the browser
• Generate summary tables from summarise_pheno()
• Preview and download export_ncbi_ast() output as TSV
• Preview and download export_ebi_ast() output as TSV
• Optionally generate EBI JSON submission files and download them as a zip archive

Run the app

Install the required packages if needed:

install.packages(c("shiny", "bslib", "DT", "remotes"))
remotes::install_github("AMRverse/AMRgen")

Then start the app from the project directory:

shiny::runApp()

Deploy to shinyapps.io

Install rsconnect if needed:

install.packages("rsconnect")

In the shinyapps.io dashboard, copy your account token details and run:

rsconnect::setAccountInfo(
  name = "<ACCOUNT>",
  token = "<TOKEN>",
  secret = "<SECRET>"
)

Then deploy this app from the project directory:

source("deploy_shinyapps.R")

Or deploy directly:

rsconnect::deployApp(appDir = ".", appName = "amrgenconverter")

Notes:

• This app depends on AMRgen, which is installed from GitHub rather than CRAN.
• If deployment fails on package restore, reinstall AMRgen locally with remotes::install_github("AMRverse/AMRgen") and redeploy.