whatbacteria

Taxon phenotype and susceptibility databases for the mirix package.

Installation

You can install the development version of whatbacteria from GitHub with:

# install.packages("devtools")
devtools::install_github("PennChopMicrobiomeProgram/whatbacteria")

To access the databases directly:

taxon_phenotypes
taxon_susceptibility

To get a particular lineage's susceptibilities:

what_antibiotic(
   c("Enterococcus faecalis", "Lactobacillus", "Lactobacillus delbrueckii"),
   "vancomycin")

To get a particular lineage's phenotypes:

what_phenotype(
   c("Bacteroidetes", "Firmicutes", "Firmicutes; Negativicutes"),
   "gram_stain")