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"One object to store them all, one object to find them, one object to query from and with ggplot2 visualize them." (Lord Sauron)

pagoo is an encapsulated, object-oriented class system for analyzing bacterial pangenomes. It uses theR6 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.

Please visitpagoo webpage for more resources.

pagoo is available at CRAN:

install.packages("pagoo")

Alternatively you can install the latest dev version from GitHub usingdevtools:

if (!require("devtools")) install.packages("devtools")devtools::install_github('iferres/pagoo')

If you usepagoo, please cite:

An object-oriented framework for evolutionary pangenome analysis.

Ignacio Ferrés, Gregorio Iraola.An object-oriented framework for evolutionary pangenome analysis.Cell Reports Methods, Volume 1, Issue 5, 2021, 100085, ISSN 2667-2375, https://doi.org/10.1016/j.crmeth.2021.100085.

The scripts that support the publication are availablehere. If you want to reproduce the analyses, aSingularity definition file to build a container with all dependencies is also provided in the above repository. An already built singularity container is hosted atsingularity-hub.

A companion protocol paper is also available:

Protocol for post-processing of bacterial pangenome data using Pagoo pipeline

Ignacio Ferrés, Gregorio Iraola.Protocol for post-processing of bacterial pangenome data using Pagoo pipeline.STAR Protocols, Volume 2, Issue 4, 2021, 100802, ISSN: 2666-1667, https://doi.org/10.1016/j.xpro.2021.100802