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methylclock

This is the development version of methylclock; for the stable release version, see methylclock.

Methylclock - DNA methylation-based clocks


Bioconductor version: Development (3.19)

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>

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews BiologicalQuestion, DNAMethylation, Normalization, Preprocessing, Software, StatisticalMethod
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
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, gridExtra, preprocessCore, dynamicTreeCut, planet
System Requirements
URL https://github.com/isglobal-brge/methylclock
Bug Reports https://github.com/isglobal-brge/methylclock/issues
See More
Suggests BiocStyle, knitr, GEOquery, rmarkdown
Linking To Rcpp
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 methylclock_1.9.0.tar.gz
Windows Binary methylclock_1.9.0.zip
macOS Binary (x86_64) methylclock_1.9.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/methylclock
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/methylclock
Bioc Package Browser https://code.bioconductor.org/browse/methylclock/
Package Short Url https://bioconductor.org/packages/methylclock/
Package Downloads Report Download Stats