oggmap is a python package that can:
- extract and assign lowest common ancestor (LCA) from orthologous groups as gene age class for a target species.
- match gene and transcript IDs and their corresponding gene age class with scRNA data sets.
- calculate and visualize transcriptome evolutionary index (TEI) on scRNA data sets.
- calculate and visualize partial transcriptome evolutionary index (TEI) profiles on scRNA data sets.
- show species lineage information from the NCBI taxonomy database.
- extract orthologous maps from OrthoFinder results.
- extract orthologous maps from eggnog_6.0 results.
- extract orthologous maps from PLAZA results.
- extract gene and transcript information from GTF files (GTF File Format).
- calculate mean/relative expression per gene age class.
- show number of expressed genes per gene age class.
Source code is available at oggmap GitHub repository and at PyPi.
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:caption: Tutorials
tutorials/index
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