Package: cascade 1.0.0

cascade: Comprehensive Analysis Suite for Cell-type specificity and Accessibility-Driven QTL Effects

Provides a hierarchical framework for systematically characterizing cell type specificity and regulatory mechanisms of molecular QTLs (molQTLs) from multiome analyses. Gene- and peak-level analyses classify eGenes and caPeaks by their cell type specificity patterns, with power-aware assessment using local false sign rates (LFSR) from multivariate adaptive shrinkage (mash) to identify likely shared but underpowered features. Variant-level analysis classifies fine-mapped variants by regulatory mechanism, with 25 mutually exclusive QTL patterns collapsing into eight mechanism categories that include three chromatin-to-expression cascade tiers.

Authors:Masahiro Kanai [aut, cre]