Pagoo

Pagoo provides an R-based, object-oriented framework for pangenome analysis that manages and analyzes bacterial molecular and phenotypic data to study genetic diversity and evolutionary patterns.

Key Features:

• Object-Oriented Design: Encapsulates pangenome data and supports storage and retrieval of raw data alongside any analysis stage within a single file format.
• Data Querying and Manipulation: Supports querying, subsetting, and comparison of pangenome datasets containing molecular and phenotypic information.
• Visualization and Statistical Analysis: Provides functionality to visualize pangenomes and perform statistical analyses on pangenome datasets.
• Integration with R Ecosystem: Interoperates with other microbial genomics packages within the R ecosystem to extend analytical capabilities.
• Scalability and Empirical Demonstration: Scales to large datasets, demonstrated by analysis of 1,000 Escherichia coli genomes and applied to a global Campylobacter fetus dataset to identify evolutionary patterns and genomic markers related to host adaptation.

Scientific Applications:

• Molecular Evolution Studies: Enables study of molecular evolution within bacterial populations by facilitating exploration of genetic diversity and tracking evolutionary changes.
• Genomic Marker Discovery: Supports identification of genomic markers and evolutionary patterns associated with host adaptation, as shown in Campylobacter fetus analyses.
• Genotype–Phenotype Analysis: Facilitates linking genomic features to phenotypic traits through integrated analysis of molecular and phenotypic data.

Methodology:

Implements an R-based object-oriented architecture that stores pangenome data in a single file format and supports querying, subsetting, comparison, visualization, and statistical analysis, with interoperability with other R microbial genomics packages.