Package: cascade
Type: Package
Title: Comprehensive Analysis Suite for Cell-type specificity and
        Accessibility-Driven QTL Effects
Version: 1.0.0
Authors@R: person("Masahiro", "Kanai", email = "mkanai@broadinstitute.org", role = c("aut", "cre"))
Description: 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.
License: MIT + file LICENSE
URL: https://github.com/mkanai/cascade
BugReports: https://github.com/mkanai/cascade/issues
OS_type: unix
SystemRequirements: C++11
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: cli, data.table (>= 1.12.0), digest, GenomicRanges, IRanges,
        jsonlite, memoise, parallel, qs2, R.utils, Rcpp, S4Vectors,
        stats, utils
Suggests: argparse, knitr, rmarkdown, testthat (>= 3.0.0)
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Config/testthat/edition: 3
LinkingTo: Rcpp
Config/pak/sysreqs: make
Repository: https://mkanai.r-universe.dev
Date/Publication: 2026-05-31 18:27:49 UTC
RemoteUrl: https://github.com/mkanai/cascade
RemoteRef: HEAD
RemoteSha: c12d2e469760731cc0993ef65bef24ddde3e3f4b
NeedsCompilation: yes
Packaged: 2026-05-31 20:10:59 UTC; root
Author: Masahiro Kanai [aut, cre]
Maintainer: Masahiro Kanai <mkanai@broadinstitute.org>