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saezlab / scverse_hackathon

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User story: get orthologs #2

Open grst opened 1 year ago

grst commented 1 year ago

It is often useful to annotate orthologous genes to leverage algorithms designed for human/mouse data.

Let's assume we have an anndata object with mouse gene ids in var_names. I would like to have a function that adds orthologous gene symbols in as an additional column: 

annotate_orthologs(
    adata, 
    source="mmu", 
    target="hsa", 
    source_identifier="ensembl",
    target_identifier="symbol", 
    key_added="human_symbol"
)
slobentanzer commented 1 year ago

this is close to https://pypath.omnipathdb.org/#homology-translation functionality. we can make a plan similar to #1. @deeenes