pagoo: 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) <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>.

Version: 0.3.13
Depends: R (≥ 3.5.0), S4Vectors, Biostrings, ggplot2
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
Published: 2022-08-31
Author: Ignacio Ferres ORCID iD [aut, cre], Gregorio Iraola ORCID iD [aut], Institut Pasteur de Montevideo [fnd]
Maintainer: Ignacio Ferres <iferres at pasteur.edu.uy>
BugReports: https://github.com/iferres/pagoo/issues
License: GPL-3
URL: https://iferres.github.io/pagoo/, https://github.com/iferres/pagoo
NeedsCompilation: no
Citation: pagoo citation info
Materials: README NEWS
CRAN checks: pagoo results

Documentation:

Reference manual: pagoo.pdf
Vignettes: Input
Methods and Plots
Querying Data
Recipes
Subseting
Quick Start

Downloads:

Package source: pagoo_0.3.13.tar.gz
Windows binaries: r-devel: pagoo_0.3.13.zip, r-release: pagoo_0.3.13.zip, r-oldrel: pagoo_0.3.13.zip
macOS binaries: r-release (arm64): pagoo_0.3.13.tgz, r-oldrel (arm64): pagoo_0.3.13.tgz, r-release (x86_64): pagoo_0.3.13.tgz, r-oldrel (x86_64): pagoo_0.3.13.tgz
Old sources: pagoo archive

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