Use scanpy hvg with batch key instead of scib package

[adamgayoso]

It would be easier to understand what's going on if this function used the scanpy hvg function

https://github.com/openproblems-bio/openproblems/blob/2d7198652875e48c63b6b6d6ab440eec27bafda0/openproblems/tasks/_batch_integration/batch_integration_graph/methods/_utils.py#L1

sc.pp.highly_variable_genes(adata, batch_key=batch, n_top_genes=G, flavor="cell_ranger")

[LuckyMD]

Good point... I think this is actually nearly equivalent to the scib function. Goekcen and I wrote this at the same time.

[github-actions[bot]]

This issue has been automatically closed because it has not had recent activity.