Issues

• Cryptic failure for download_ebi when function returns a table of 0 rows

  AMRverse/AMRgen#113 · Filter by author jhawkey opened on Jul 8, 2026

• Make some of the imports optional

  AMRverse/AMRgen#112 · Filter by author evolarjun opened on May 28, 2026

• add function to fetch genotype data from Allthebacteria

  AMRverse/AMRgen#110 · Filter by author katholt opened on May 13, 2026
  

• Add minor errors to concordance function

  AMRverse/AMRgen#109 · Filter by author katholt opened on May 13, 2026
  

• Add drug as a parameter in the summarise_geno_pheno() function

  AMRverse/AMRgen#95 · Filter by author natacha-couto opened on Mar 19, 2026

• amr_upset() - MIC distribution panel - box plot middle line is not plotting the median?

  AMRverse/AMRgen#93 · Filter by author karatsang opened on Mar 19, 2026
  1

• check_binary_matrix fails if no 'mic' column

  AMRverse/AMRgen#92 · Filter by author katholt opened on Mar 18, 2026

• concordance() - nice to have : exclude_markers filter by list of core genes

  AMRverse/AMRgen#60 · Filter by author silargi opened on Feb 18, 2026

• add function to download Allthebacteria AMRfp data

  AMRverse/AMRgen#46 · Filter by author katholt opened on Feb 10, 2026

• download_ebi() function: Warnings in mutate()

  AMRverse/AMRgen#43 · Filter by author silargi opened on Feb 6, 2026
  2

• Sulfonamide to it's own "drug_class"?

  AMRverse/AMRgen#35 · Filter by author evolarjun opened on Jan 5, 2026
  2

• Generalise upset plot function to accept any genotype and quantitative phenotype

  AMRverse/AMRgen#33 · Filter by author MaxWallat opened on May 20, 2025

• Tree vs geno & pheno

  AMRverse/AMRgen#32 · Filter by author meganecarey opened on May 20, 2025

• get_binary_matrix - to do list

  AMRverse/AMRgen#29 · Filter by author katholt opened on Mar 23, 2025

• Implement unit testing

  AMRverse/AMRgen#24 · Filter by author msberends opened on Feb 5, 2025
  

• Replace old functions

  AMRverse/AMRgen#23 · Filter by author msberends opened on Feb 5, 2025
  

• amr_logistic function

  AMRverse/AMRgen#20 · Filter by author katholt opened on Feb 4, 2025
  1

• consider how to handle 'nested' drug classes

  AMRverse/AMRgen#10 · Filter by author katholt opened on Jan 23, 2025

• expand genotype importer to parse CARD & resfinder

  AMRverse/AMRgen#7 · Filter by author katholt opened on Jan 17, 2025
  

• add functions for identifying core genes using NCBI hierarchy

  AMRverse/AMRgen#5 · Filter by author katholt opened on Jan 16, 2025
  

• Shiny app

  AMRverse/AMRgen#2 · Filter by author jhawkey opened on Jan 14, 2025