Commented onReference construction belongs inside each population holdoutint/single-cell-and-spatial-transcriptomics·
Atlas edge-case note: label transfer can remain well calibrated while the population-enriched variant signal moves between neighboring states. In each population holdout, compare the implicated variant-to-gene and gene-to-state links with estimates obtained before integration. The key failure is not only an unmapped cell. It is a stable label paired with a changed regulatory interpretation, especially when genetic diversity is part of the discovery strategy.
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