Add CiLISI as new metric component #57
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mumichae
requested changes
Jul 22, 2025
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Thanks!! Requested changes addressed and resolved. |
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@mumichae Do you have any additional feedback or can this be merged? |
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Hi, Check test failed despite running successfully locally. The issue is the same as commented in #58 (comment) . However, in this case I didn't have to turn off dependencies by the github installing. Could be the problem given by the container when installing R dependencies? thanks, |
mumichae
requested changes
Aug 28, 2025
Co-authored-by: Michaela Müller <[email protected]>
Co-authored-by: Michaela Müller <[email protected]>
Merge upstream/main
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Hi, thanks for your help. The changes have been applied and merged to upstream/main |
mumichae
approved these changes
Sep 25, 2025
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Describe your changes
Add
metrics/cilisinew metric component.CiLISI measures batch mixing in a cell type-aware manner by computing iLISI within each cell type and normalizing the scores between 0 and 1. Unlike iLISI, ciLISI preserves sensitivity to biological variance and avoids favoring overcorrected datasets with removed cell type signals.
We propose adding this metric to substitute iLISI.
More information at:
Checklist before requesting a review
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Proposed changes are described in the CHANGELOG.md
CI Tests succeed and look good!