Welcome to oggmap’s documentation!
What is oggmap?
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.
Table of Contents
Documentation
Tutorials