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cff-version: 1.2.0
message: 'To cite package "cascade" in publications use:'
type: software
license: MIT
title: 'cascade: Comprehensive Analysis Suite for Cell-type specificity and Accessibility-Driven
  QTL Effects'
version: 1.0.0
doi: 10.32614/CRAN.package.cascade
abstract: 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:
- family-names: Kanai
  given-names: Masahiro
  email: mkanai@broadinstitute.org
repository: https://mkanai.r-universe.dev
repository-code: https://github.com/mkanai/cascade
commit: c12d2e469760731cc0993ef65bef24ddde3e3f4b
url: https://github.com/mkanai/cascade
date-released: '2026-05-31'
contact:
- family-names: Kanai
  given-names: Masahiro
  email: mkanai@broadinstitute.org