Analyze Bacterial Pangenomes in R with 'Pagoo'

Provides an encapsulated, object-oriented class system for analyzing bacterial pangenomes. For a definition of this concept, see Tettelin, et al. (2005) . 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), .


Reference manual

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0.3.9 by Ignacio Ferres, 9 months ago,

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Authors: Ignacio Ferres [aut, cre] , Gregorio Iraola [aut] , Institut Pasteur de Montevideo [fnd]

Documentation:   PDF Manual  

GPL-3 license

Imports R6, reshape2, vegan, GenomicRanges, BiocGenerics, shinyWidgets, shinydashboard, DT, plotly, magrittr, heatmaply, dendextend, ggfortify, shiny

Depends on S4Vectors, Biostrings, ggplot2

Suggests micropan, patchwork, ape, phangorn, pegas, DECIPHER, rhierbaps, IRanges, knitr, rmarkdown, testthat, covr

See at CRAN