Package: pagoo
Version: 0.3.17
Title: Analyze Bacterial Pangenomes in R with 'Pagoo'
Description: 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>.
Authors@R: c(
    person("Ignacio", "Ferres", , "iferres@pasteur.edu.uy", role =  c("aut", "cre"), 
      comment = c(ORCID = "0000-0003-0910-6568")
    ),
    person("Gregorio", "Iraola", , "iferres@pasteur.edu.uy", role = c("aut"), 
      comment = c(ORCID = "0000-0002-6516-3404")
    ),
    person("Institut Pasteur de Montevideo", role = c("fnd")
    )
  )
Maintainer: Ignacio Ferres <iferres@pasteur.edu.uy>
URL: https://iferres.github.io/pagoo/, https://github.com/iferres/pagoo
BugReports: https://github.com/iferres/pagoo/issues
Depends: R (>= 3.5.0), S4Vectors, Biostrings, ggplot2
biocViews:
Imports: R6, reshape2, vegan, GenomicRanges, BiocGenerics,
        shinyWidgets, shinydashboard, DT, plotly, magrittr, heatmaply,
        dendextend, ggfortify, shiny
Suggests: micropan, patchwork, ape, phangorn, pegas, DECIPHER,
        rhierbaps, IRanges, knitr, rmarkdown, testthat, covr
License: GPL-3
Encoding: UTF-8
ByteCompile: true
RoxygenNote: 7.2.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-11-18 18:24:46 UTC; iferres
Author: Ignacio Ferres [aut, cre] (<https://orcid.org/0000-0003-0910-6568>),
  Gregorio Iraola [aut] (<https://orcid.org/0000-0002-6516-3404>),
  Institut Pasteur de Montevideo [fnd]
Repository: CRAN
Date/Publication: 2022-11-18 18:50:02 UTC
Built: R 4.3.0; ; 2023-07-10 07:11:14 UTC; unix
