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pagoo

A comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.

https://github.com/iferres/pagoo

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.3%) to scientific vocabulary

Keywords

bioinformatics microbial-genomics pangenome r r6 rstats
Last synced: 10 months ago · JSON representation

Repository

A comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.

Basic Info
Statistics
  • Stars: 22
  • Watchers: 2
  • Forks: 4
  • Open Issues: 11
  • Releases: 0
Topics
bioinformatics microbial-genomics pangenome r r6 rstats
Created over 7 years ago · Last pushed over 3 years ago
Metadata Files
Readme

README.md

R-CMD-check pkgdown codecov <!-- badges: end -->

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: r install.packages("pagoo")

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

Owner

  • Name: Ignacio Ferrés
  • Login: iferres
  • Kind: user
  • Location: Montevideo - Uruguay
  • Company: Institut Pasteur Montevideo

Bioinformatics. Research assistant at Institut Pasteur Montevideo (Uruguay), Bioinformatics Unit, Microbial Genomics Lab

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 425
  • Total Committers: 1
  • Avg Commits per committer: 425.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 10
  • Committers: 1
  • Avg Commits per committer: 10.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
iferres i****s@g****m 425

Issues and Pull Requests

Last synced: about 2 years ago

All Time
  • Total issues: 22
  • Total pull requests: 43
  • Average time to close issues: 2 months
  • Average time to close pull requests: about 2 hours
  • Total issue authors: 13
  • Total pull request authors: 1
  • Average comments per issue: 5.36
  • Average comments per pull request: 0.14
  • Merged pull requests: 41
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 3
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • iferres (10)
  • g1o (1)
  • emilywollmuth (1)
  • alegione (1)
  • MauriAndresMU1313 (1)
  • LovaRandriantseheno (1)
  • hayleyjaywilson (1)
  • diaspj (1)
  • sushanta26 (1)
  • qisun2 (1)
  • eam12 (1)
  • jhcuarta (1)
  • neelam19051 (1)
  • herber4 (1)
Pull Request Authors
  • iferres (43)
Top Labels
Issue Labels
enhancement (7) bug (3) low-priority (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 255 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 5
  • Total maintainers: 1
cran.r-project.org: pagoo

Analyze Bacterial Pangenomes in R with 'Pagoo'

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 255 Last month
Rankings
Stargazers count: 11.5%
Forks count: 12.2%
Dependent repos count: 23.9%
Average: 24.8%
Dependent packages count: 28.7%
Downloads: 48.0%
Maintainers (1)
iferres@pasteur.edu.uy
Last synced: about 2 years ago

Dependencies

DESCRIPTION cran
  • Biostrings * depends
  • R >= 3.5.0 depends
  • S4Vectors * depends
  • ggplot2 * depends
  • BiocGenerics * imports
  • DT * imports
  • GenomicRanges * imports
  • R6 * imports
  • dendextend * imports
  • ggfortify * imports
  • heatmaply * imports
  • magrittr * imports
  • plotly * imports
  • reshape2 * imports
  • shiny * imports
  • shinyWidgets * imports
  • shinydashboard * imports
  • vegan * imports
  • DECIPHER * suggests
  • IRanges * suggests
  • ape * suggests
  • covr * suggests
  • knitr * suggests
  • micropan * suggests
  • patchwork * suggests
  • pegas * suggests
  • phangorn * suggests
  • rhierbaps * suggests
  • rmarkdown * suggests
  • testthat * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite