Add Mixscale continuous scoring; restructure into a perturbation-efficacy tutorial#64
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Add Mixscale continuous scoring; restructure into a perturbation-efficacy tutorial#64Zethson wants to merge 1 commit into
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Generalize the title and intro, group the binary classification (Mixscape) and the new continuous scoring (Mixscale) under two sections, and rename the notebook to perturbation_efficacy.ipynb. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Adds pt.tl.Mixscale for continuous per-cell perturbation scoring (Jiang et al., Nature Cell Biology 2025), matching the satijalab/Mixscale R implementation to floating-point precision. Mixscape is refactored into a _perturbation_screen package: a shared PerturbationScreenAnalyzer base (perturbation_signature + DE marker detection) with Mixscape (binary) and Mixscale (continuous) as siblings. pt.tl.Mixscape is unchanged. Renames the tutorial to perturbation_efficacy and bumps the pertpy-tutorials submodule to the matching commit (scverse/pertpy-tutorials#64). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Generalizes the mixscape tutorial to cover both perturbation-efficacy methods and adds a Mixscale section.
pt.tl.Mixscale().mixscale(...)and shows that the continuous score separates KO from NP cells within a target gene.mixscape.ipynb->perturbation_efficacy.ipynb(executed end-to-end).Pairs with the pertpy PR adding
pt.tl.Mixscale(scverse/pertpy#945); that PR bumps this submodule to the merged commit.🤖 Generated with Claude Code