Package: causalASCEND
Type: Package
Title: Scalable Two-Tier Causal Discovery for Multi-Omic Data
Version: 0.99.1
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 (cause-before-effect)
        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 (>= 4.5.0)
License: GPL-3
Encoding: UTF-8
Imports: methods, stats, SummarizedExperiment, utils
Suggests: BiocStyle, knitr, MultiAssayExperiment, rmarkdown, 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'
Config/pak/sysreqs: zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-20 12:19:14 UTC
RemoteUrl: https://github.com/BiocStaging/causalASCEND
RemoteRef: HEAD
RemoteSha: dcd3578c54be426b85c3803c1d22c4e390cdf516
NeedsCompilation: no
Packaged: 2026-10-20 15:21:33 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>