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

Need some help? Ask on the Bioconductor Support site!

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

Suggests	BiocStyle, randomForest, testthat, knitr, rmarkdown, e1071, xgboost, keras, tensorflow
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

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/
Package Downloads Report	Download Stats