oggmap

oggmap integrates gene age information per orthogroup with single-cell RNA sequencing (scRNA-seq) data to enable evolutionary analysis of transcriptomic datasets.

Key Features:

• Orthomap Extraction: Extracts orthomaps mapping gene ages per orthogroup for specified query species using data from OrthoFinder, eggNOG, and PLAZA.
• Extensive Species Coverage: Provides gene age information for over a thousand eukaryotic species, covering both model and non-model organisms.
• Integration with scRNA-seq Data: Calculates gene age-weighted expression profiles from scRNA-seq objects using the Scanpy toolkit.
• Visualization Capabilities: Produces visualizations of gene categories such as age class and nucleotide diversity bins to examine expression profiles across cells.

Scientific Applications:

• Evolutionary context of development: Contextualizes cellular differentiation and ontogeny within an evolutionary framework by linking gene age to cell states.
• Ancient gene contribution analysis: Assesses how ancient genes contribute to modern cell functions and phenotypes.
• Study of evolutionary constraints: Investigates evolutionary pressures and constraints that shape organismal complexity via transcriptomic patterns.

Methodology:

Extracts orthogroup-based gene ages from OrthoFinder, eggNOG, and PLAZA and integrates these data with scRNA-seq datasets to compute age-weighted expression profiles using the Scanpy toolkit.