Opinionated defaults for 2.0
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@flying-sheep is already working on this.
Since Apr 2, 2026.
Area – API
- Dominant language
- Python
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Description
Some functions can be given defaults that depend on conventions
-
layer="counts"for platform-specific read functions (i.e. not any matrix, but 10x matrices) -
mask_var="highly_variable"inRankGenesGroupsPreset- and PCA (was already the case, maybe make it a hard fail if hvg wasn’t run and
mask_varisn’t changed?)
- and PCA (was already the case, maybe make it a hard fail if hvg wasn’t run and
-
tie_correct=TrueinRankGenesGroupsPreset?
more?
threads:
- https://theislab-munich.slack.com/archives/C04U6DW20NB/p1774522763964959
- https://scverse.zulipchat.com/#narrow/channel/328272-scanpy/topic/What.20are.20your.20favourite.20defaults.20.2F.20replacements.20for.202.2E0.3F/with/584681746
So far: https://scanpy.readthedocs.io/en/latest/generated/scanpy.Preset.html
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