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As we are refactoring scvi, I'm wondering what the utility would be to spin off the i/o part of scanpy into it's own lightweight package that's more general for reading single cell pipeline outputs into anndata. For example, we'd like to use the scanpy read from 10x/visium functions, but don't necessarily want to have scanpy be a full requirement. It's also a bit confusing why something like read_umi_tools
is in anndata but not read_10x_h5
. The same goes for loom to some extent. I could imagine either moving such functionality to anndata or a standalone package that could be expanded to include support for other technologies like scATAC-seq.
This overall could be a big benefit to methods developers who would like to build on anndata.
LustigePerson, grst, rcannood, gokceneraslan and gszep