orthogene

orthogene maps orthologous genes across 700+ organisms and provides utility functions to aggregate or expand data.frames, gene expression matrices, and lists using 1:1, many:1, 1:many, or many:many gene mappings both within and between species.

Key Features:

• Cross-species ortholog mapping: Pulls up-to-date gene ortholog mappings across more than 700 organisms.
• Flexible gene relationship handling: Supports 1:1, many:1, 1:many, and many:many gene mappings for both within-species and between-species analyses.
• Data structure transformation: Aggregates or expands common objects including data.frames, gene expression matrices, and lists into analysis-ready formats.
• Automated standardization: Integrates automated species and identifier standardization and homolog inference across multiple databases.

Scientific Applications:

• Cross-species gene expression analysis: Transforms gene lists, tables, and high-dimensional matrices for comparative transcriptomics across species.
• Ortholog inference: Enables transparent and scalable homolog mapping in bioinformatics workflows involving non-one-to-one homolog relationships.

Methodology:

orthogene integrates automated species and identifier standardization with homolog inference across multiple databases, abstracting technical complexity while retaining user control over ambiguous homolog relationships.