orthogene: a Bioconductor package to easily map genes within and across hundreds of species

Abstract

MotivationMapping genes across identifier systems and species is a routine but critical step in bioinformatics workflows. Despite its ubiquity, gene mapping is frequently handled using bespoke, ad hoc solutions, increasing duplicated effort and introducing opportunities for error. These issues are exacerbated by the prevalence of non-one-to-one homolog relationships and inconsistent handling of gene identifiers across species and databases, which can compromise downstream analyses and reproducibility. ResultsWe present orthogene, an R/Bioconductor package that simplifies gene mapping within and across hundreds of species. orthogene provides a unified, workflow-oriented framework that integrates automated species and identifier standardization, homolog inference across multiple databases, flexible handling of ambiguous homolog relationships, and transformation of gene lists, tables, and high-dimensional matrices into analysis-ready formats. By abstracting common sources of technical complexity while retaining user control, orthogene enables transparent, reproducible, and scalable gene mapping across a wide range of biological contexts. Availabilityhttps://bioconductor.org/packages/orthogene Contactbrian_schilder@alumni.brown.edu