Package: causalASCEND
Type: Package
Title: Scalable Two-Tier Causal Discovery for Multi-Omic Data
Version: 0.99.0
Authors@R: c(
    person("Stephen", "Asiedu", role = c("aut", "cre"),
        email = "stephen.asiedu@kcl.ac.uk",
        comment = c(ORCID = "0009-0005-8885-5381")),
    person("David", "Watson", role = "aut",
        email = "david.watson@kcl.ac.uk"))
Description: Causal ASCEND (Ancestral Scalable Causal discovEry via
        iNherited Descent) infers ancestral relations among downstream
        molecular variables, such as gene expression, when a layer of
        upstream variables, such as genotypes or methylation sites, is
        known to precede them. Each conditional independence test
        conditions only on a small, iteratively refined set of nearest
        ancestors instead of the whole upstream layer, so the number of
        tests grows polynomially with the number of variables. The
        package accepts matrices, SummarizedExperiment objects or a
        MultiAssayExperiment, and returns the ancestral relations with
        the rule and evidence behind each one.
Depends: R (>= 4.3.0)
License: GPL-3
Encoding: UTF-8
Imports: methods, stats, utils
Suggests: BiocStyle, knitr, MultiAssayExperiment, rmarkdown,
        SummarizedExperiment, testthat (>= 3.0.0)
VignetteBuilder: knitr
biocViews: GraphAndNetwork, NetworkInference, Network, SystemsBiology,
        GeneExpression, Transcriptomics, SNP, GeneticVariability,
        MultipleComparison, Software
URL: https://github.com/SparkAILab/causalASCEND
BugReports: https://github.com/SparkAILab/causalASCEND/issues
Config/testthat/edition: 3
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Collate: 'AllClasses.R' 'accessors.R' 'ascend.R'
        'causalASCEND-package.R' 'engine.R' 'evaluate.R' 'simulate.R'
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-14 18:34:33 UTC
RemoteUrl: https://github.com/BiocStaging/causalASCEND
RemoteRef: HEAD
RemoteSha: c780ecd145e2db60fd9a57f5525bd1ca801a90b0
NeedsCompilation: no
Packaged: 2026-10-14 22:31:26 UTC; root
Author: Stephen Asiedu [aut, cre] (ORCID:
    <https://orcid.org/0009-0005-8885-5381>),
  David Watson [aut]
Maintainer: Stephen Asiedu <stephen.asiedu@kcl.ac.uk>