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Pagoo: An encapsulated OO class system 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

Currently, pagoo is only available at GitHub. The easiest way to install this package is by using devtools:

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

We test pagoo in the three main operating systems (linux, macOS, and Windows). We plan to put the code in CRAN and/or Bioconductor repositories in the future.