An object-oriented framework for evolutionary pangenome analysis.
R
bacterial comparative genomics
bacterial evolution
data visualization
object-oriented programming
pangenome analysis
pangenome reconstruction
Journal
Cell reports methods
ISSN: 2667-2375
Titre abrégé: Cell Rep Methods
Pays: United States
ID NLM: 9918227360606676
Informations de publication
Date de publication:
27 09 2021
27 09 2021
Historique:
received:
09
03
2021
revised:
04
06
2021
accepted:
25
08
2021
entrez:
27
4
2022
pubmed:
28
4
2022
medline:
28
4
2022
Statut:
epublish
Résumé
Pangenome analysis is fundamental to explore molecular evolution occurring in bacterial populations. Here, we introduce Pagoo, an R framework that enables straightforward handling of pangenome data. The encapsulated nature of Pagoo allows the storage of complex molecular and phenotypic information using an object-oriented approach. This facilitates to go back and forward to the data using a single programming environment and saving any stage of analysis (including the raw data) in a single file, making it sharable and reproducible. Pagoo provides tools to query, subset, compare, visualize, and perform statistical analyses, in concert with other microbial genomics packages available in the R ecosystem. As working examples, we used 1,000
Identifiants
pubmed: 35474671
doi: 10.1016/j.crmeth.2021.100085
pii: S2667-2375(21)00140-5
pmc: PMC9017228
doi:
Banques de données
figshare
['10.6084/m9.figshare.13622354.v1']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Pagination
100085Informations de copyright
© 2021 The Authors.
Déclaration de conflit d'intérêts
The authors declare no competing interests.
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