Package: CytoMethIC
Type: Package
Title: DNA methylation-based machine learning models
Description: This package provides model data and functions for easily
        using machine learning models that use data from the DNA
        methylome to classify cancer type and phenotype from a sample.
        The primary motivation for the development of this package is
        to abstract away the granular and accessibility-limiting code
        required to utilize machine learning models in R. Our package
        provides this abstraction for RandomForest, e1071 Support
        Vector, Extreme Gradient Boosting, and Tensorflow models. This
        is paired with an ExperimentHub component, which contains
        models developed for epigenetic cancer classification and
        predicting phenotypes. This includes CNS tumor classification,
        Pan-cancer classification, race prediction, cell of origin
        classification, and subtype classification models. The package
        links to our models on ExperimentHub. The package currently
        supports HM450, EPIC, EPICv2, MSA, and MM285.
Version: 1.9.0
Authors@R: c(person("Wanding", "Zhou", role = c("aut"),
             email = "zhouwanding@gmail.com", comment = c(ORCID = "0000-0001-9126-1932")),
             person("Jacob", "Fanale", role = c("aut", "cre"), email = "jfanale@seas.upenn.edu",
              comment = c(ORCID = "0009-0002-0490-3269")))
License: Artistic-2.0
Depends: R (>= 4.4.0), ExperimentHub
Imports: utils, stats, tools, sesame, methods, sesameData,
        BiocParallel, BiocManager
VignetteBuilder: knitr
Suggests: tibble, BiocStyle, randomForest, testthat, knitr, rmarkdown,
        e1071, xgboost, keras, tensorflow
URL: https://github.com/zhou-lab/CytoMethIC
BugReports: https://github.com/zhou-lab/CytoMethIC/issues
biocViews: ExperimentData, MicroarrayData, Genome, ExperimentHub,
        MethylationArrayData, CancerData, PackageTypeData
NeedsCompilation: no
RoxygenNote: 7.3.2
Encoding: UTF-8
Packaged: 2026-10-10 10:46:04 UTC; root
Config/pak/sysreqs: libicu-dev libpng-dev libssl-dev libx11-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:37:28 UTC
RemoteUrl: https://github.com/bioc/CytoMethIC
RemoteRef: HEAD
RemoteSha: 193109c97eee860a2acb38e1f8bbcdb1096c8200
Author: Wanding Zhou [aut] (ORCID: <https://orcid.org/0000-0001-9126-1932>),
  Jacob Fanale [aut, cre] (ORCID:
    <https://orcid.org/0009-0002-0490-3269>)
Maintainer: Jacob Fanale <jfanale@seas.upenn.edu>
