DESCRIPTION

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: 1.3.3
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: 2023-11-10 21:18:41 UTC; jfanale