ArticleCell reports methods2021
An object-oriented framework for evolutionary pangenome analysis.
Article in Cell reports methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Geographic clustering and population structures ofMicrobial genomics · 2026Article
- Integrative phylogenomic and pangenome landscape of Bacillus: insights from 10,000 genomes into taxonomy, functional potential, and biotechnological applications.World journal of microbiology & biotechnology · 2026Article
- Comparative Genome Analysis and Characterization of Lacticaseibacillus Paracasei NKN344 Strain Isolated from Curd of Buffalo Milk Reared on Brackish Water Lagoons of the Eastern Indian Coast.Probiotics and antimicrobial proteins · 2026Article
- Phylogenomics and gene association analysis support probiotic potential in a subset ofMicrobial genomics · 2026Article
- Sheep-associated Escherichia coli in Albania show high genomic similarity to European ovine lineages and a conserved core resistome.FEMS microbiology letters · 2026Article
- Genomic evolution ofApplied and environmental microbiology · 2025Article
- Interred mechanisms of resistance and host immune evasion revealed through network-connectivity analysis ofmSystems · 2025Article
- Unveiling novel features and phylogenomic assessment of indigenousMicrobiology spectrum · 2025Article
- Relating ecological diversity to genetic discontinuity across bacterial species.Genome biology · 2025Article
- Seven quick tips for gene-focused computational pangenomic analysis.BioData mining · 2024Article
- Genome and Compound Analysis of Sioxanthin-Producing Marine Actinobacterium Micromonospora sp. nov. Strain SH-82 Isolated from Sponge Scopalina hapalia.Current microbiology · 2024Article
- Time-calibrated phylogenetic and chromosomal mobilome analyses of Staphylococcus aureus CC398 reveal geographical and host-related evolution.Nature communications · 2024Article
- Article
- Zoonotic bacterial and parasitic intestinal pathogens in foxes, raccoons and other predators from eastern Germany.Environmental microbiology reports · 2024Article
- Unveiling genome plasticity and a novel phage inMicrobial genomics · 2024Article
- Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals.Microbial genomics · 2024Article
- Article
- Whole-genome sequencing provides insights into a novel species:Microbiology spectrum · 2023Article
- Characterization of the probiotic properties ofFrontiers in microbiology · 2023Article
- Genomic analysis of two Bacillus safensis isolated from Merzouga desert reveals desert adaptive and potential plant growth-promoting traits.Functional & integrative genomics · 2022Article
Corrections and comments
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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
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