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What's Changed
Filtering of Cells and Samples for CiLISI:
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Added a filtering step to ensure that only cell types with a minimum number of cells are included in the CiLISI computation (default = 10). This helps to exclude low-frequency cell types.
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Implemented a filter for minimum sample size to ensure that each cell type has sufficient representation across samples for meaningful validation and consistency assessment (default = min 2 samples with such cell type).