The goal of pdallele is to simplify the downloading, cleanup, and analysis of NCBI Pathogen Detection data, primarailly for exploring the diversity and distribution antimicrobial resistance alleles across large numbers of bacterial isolates.
You can install the development version of pdallele from GitHub with:
# install.packages("devtools")
devtools::install_github("armack/pdallele")No CRAN release in planned.
This contains all the code the code used to generate the tables and figures in "β-Lactamase Diversity in Acinetobacter baumannii and Pseudomonas aeruginosa: A Bioinformatic Analysis" by Mack et al.
Data downloading, processing, and cleanup was performed as outlined in
vignette("downloading-data", package = "pdallele") and
vignette("processing-data", package = "pdallele").
The code used for analysis and generation of tables and figures is included in
vignette("sample-analysis"", package = "pdallele") and
vignette("additional-analysis", package = "pdallele").
This code is available on Zenodo at https://zenodo.org/doi/10.5281/zenodo.10476134 and by DOI 10.5281/zenodo.10476135
Citation information for the preprint and final versions of the manuscript will added when available