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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 (3.18)

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 "4.3") 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 1.7.0
In Bioconductor since BioC 3.14 (R-4.1) (2 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
Linking To Rcpp
Suggests BiocStyle, knitr, GEOquery, rmarkdown
System Requirements
Enhances
URL https://github.com/isglobal-brge/methylclock
Bug Reports https://github.com/isglobal-brge/methylclock/issues
See More
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_1.7.0.tar.gz
Windows Binary methylclock_1.7.0.zip
macOS Binary (x86_64) methylclock_1.7.0.tgz
macOS Binary (arm64) methylclock_1.7.0.tgz
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