Pagoo: An encapsulated Object-Oriented framework for analyzing bacterial pangenomes in R

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

Introduction

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

Information and Tutorials

Please visit pagoo webpage for more resources.

Installation

pagoo is available at CRAN:

install.packages("pagoo")

Alternatively you can install the latest dev version from GitHub using devtools:

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

Citation

If you use pagoo, 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 available here. If you want to reproduce the analyses, a Singularity definition file to build a container with all dependencies is also provided in the above repository. An already built singularity container is hosted at singularity-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