filter_rank_genes_groups much slower than rank_genes_groups
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Description
I was using Scanpy 1.5.0
It took me more than two hours to finish filter_rank_genes_groups with default parameters while rank_genes_groups takes less than 5 minutes.
But theoretically, it shouldn't be too different from rank_genes_groups right?
But it seems way slower than rank_genes_groups and much slower than Seurat.
Is there a way to make it faster?
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First steps
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Research direction
Start by reproducing the reported timing difference between filter_rank_genes_groups and rank_genes_groups in Scanpy 1.5.0 using their default parameters. Compare the two function entry points and identify where the extra runtime occurs; done means the performance difference is explained and a faster, validated behavior is demonstrated.
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Assessment
- Tech stack
- python
- Domain
- data, performance
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100