pagoo

Provides an encapsulated, object-oriented class system for analyzing bacterial pangenomes. For a definition of this concept, see Tettelin, et al. (2005) doi:10.1073/pnas.0506758102. It uses the R6 package as backend. It was designed in order to facilitate and speed-up the comparative analysis of multiple bacterial genomes, standardizing and optimizing routine tasks performed everyday. There are a handful of things done everyday when working with bacterial pangenomes: subset, summarize, extract, visualize and store data. So, 'pagoo' is intended to facilitate these tasks as much as possible. For a description of the implemented data structure and methods, see Ferres & Iraola (2020), doi:10.1101/2020.07.29.226951.