Add residual design-effect correction and aggregation calibration parameters - #146

Merged

ammarcsj merged 7 commits into

mainfrom

add_residual_deff_correction

Jul 31, 2026

Commits on Jul 31, 2026

Add explicit median_normalization option
ammarcsj
committed
330ca98
Make per-protein peptide cap configurable
ammarcsj
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cbe7b95
Extend residual decorrelation cutoff grid and expose it as a parameter
ammarcsj
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5069a90
Cap samples used for the sibling-correlation estimate
ammarcsj
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b94b133
Aggregate via median when pruning collapses a parent to one child
ammarcsj
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a2c6d38
Add residual design-effect correction at the between-peptide level
ammarcsj
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c7bd007
Save residual decorrelation diagnostic plots when runtime_plots is set
ammarcsj
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632e92b