CytoMethIC

DNA methylation-based classification and regression


Bioconductor version: Release (3.19)

This package provides DNA methylation-based prediction of cancer type, molecular signature and clinical outcomes. It provides convenience functions for missing value imputation, probe ID conversion, model interpretation and visualization. The package links to our models on ExperimentHub. The package currently supports HM450, EPIC and EPICv2.

Author: Wanding Zhou [aut] , Jacob Fanale [aut, cre]

Maintainer: Jacob Fanale <jfanale at seas.upenn.edu>

Citation (from within R, enter citation("CytoMethIC")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CytoMethIC")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CytoMethIC")
CytoMethIC User Guide HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CancerData, ExperimentData, ExperimentHub, Genome, MethylationArrayData, MicroarrayData, PackageTypeData
Version 1.0.0
License Artistic-2.0
Depends R (>= 4.4.0), ExperimentHub
Imports tibble, utils, stats, tools, sesame, methods, sesameData, BiocParallel, BiocManager
System Requirements
URL https://github.com/zhou-lab/CytoMethIC
Bug Reports https://github.com/zhou-lab/CytoMethIC/issues
See More
Suggests BiocStyle, randomForest, testthat, knitr, rmarkdown, e1071, xgboost, keras, tensorflow
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CytoMethIC_1.0.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/CytoMethIC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CytoMethIC
Package Short Url https://bioconductor.org/packages/CytoMethIC/
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