methylclock

DOI: 10.18129/B9.bioc.methylclock    

Methylclock - DNA methylation-based clocks

Bioconductor version: Release (3.14)

This package allows to estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks. Chronological DNAm age (in years) : Horvath's clock, Hannum's clock, BNN, Horvath's skin+blood clock, PedBE clock and Wu's clock. Gestational DNAm age : Knight's clock, Bohlin's clock, Mayne's clock and Lee's clocks. Biological DNAm clocks : Levine's clock and Telomere Length's clock.

Author: Dolors Pelegri-Siso [aut, cre], Juan R. Gonzalez [aut]

Maintainer: Dolors Pelegri-Siso <dolors.pelegri at isglobal.org>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("methylclock")

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("methylclock")

 

HTML	R Script	DNAm age using diffrent methylation clocks
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	BiologicalQuestion, DNAMethylation, Normalization, Preprocessing, Software, StatisticalMethod
Version	1.0.1
In Bioconductor since	BioC 3.14 (R-4.1) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.1.0), methylclockData, devtools, quadprog
Imports	Rcpp (>= 1.0.6), ExperimentHub, dplyr, impute, PerformanceAnalytics, Biobase, ggpmisc, tidyverse, ggplot2, ggpubr, minfi, tibble, RPMM, stats, graphics, tidyr, preprocessCore, dynamicTreeCut
LinkingTo	Rcpp
Suggests	BiocStyle, knitr, GEOquery, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/isglobal-brge/methylclock
BugReports	https://github.com/isglobal-brge/methylclock/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	methylclock_1.0.1.tar.gz
Windows Binary	methylclock_1.0.1.zip
macOS 10.13 (High Sierra)	methylclock_1.0.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/methylclock
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/methylclock
Package Short Url	https://bioconductor.org/packages/methylclock/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive