DESCRIPTION

Package: pagoo
Version: 0.3.18
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: 7.2.3
Roxygen: list(r6 = TRUE)
VignetteBuilder: knitr