"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 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.
Please visit pagoo webpage for more resources.
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')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