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 (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 (>= 4.3.0)
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'
