IntegrateRigor: annotation-free integration optimization for cell identity recovery reveals cancer-immune interface niches (opens in new tab)

Integrating single-cell and spatial transcriptomics data across batches is essential for recovering comparable cell identities (including cell types, subtypes, and states) as a prerequisite for downstream analyses in multi-condition and large-scale studies. This task remains challenging because between-batch variation removal often conflicts with cell identity preservation, and current methods typically rely on generic highly variable gene selection and lack principled metrics for hyperparame...