scverse / scverse/scanpy

Option to return sparse arrays from `sc.get.aggregate`

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#2,898 3 comments 0 reactions 1 assignee View on GitHub

@Intron7 is already working on this.

Since Jan 23, 2025.

Area – API
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Python
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Description

What kind of feature would you like to request?

Additional function parameters / changed functionality / changed defaults?

Please describe your wishes

@Intron7, found a use case 😆

It could be nice for sc.get.aggregate to be able to return sparse matrices where we don't expect the aggregation to return very dense data.

Previously discussed in:

Usecases include:

This would require both api design choices for what the argument is called, and efficient implementations for both dense and sparse results (python-graphblas could be useful here)

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