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Free keywords:
gene-expression, scrna-seq-analysis, phylostratigraphy, evolution, orthofinder, orthomap
Abstract:
For model species, single-cell RNA-based cell atlases are available. A good cell atlas includes all major stages in a species’ ontogeny, and soon, they will be standard even for non-model species. Here, we propose a Python package called oggmap, which allows for the easy extraction of an orthomap (gene ages per orthogroup) for any given query species from OrthoFinder and other gene family data resources, like homologous groups from eggNOG or PLAZA. oggmap provides extracted gene ages for more than thousand eukaryotic species which can be further used to calculate gene age-weighted expression data from scRNA sequencing objects using the Python Scanpy toolkit. Not limited to one transcriptome evolutionary index, oggmap can visualize the individual gene category (e.g. age class, nucleotide diversity bin) and their corresponding expression profiles to investigate scRNA-based cell type assignments in an evolutionary context.
