methylclock

Methylclock - DNA methylation-based clocks


Bioconductor version: Release (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")

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 1.10.0
In Bioconductor since BioC 3.14 (R-4.1) (3 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
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Suggests BiocStyle, knitr, GEOquery, rmarkdown
Linking To Rcpp
Enhances
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Package Archives

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

Source Package methylclock_1.10.0.tar.gz
Windows Binary methylclock_1.10.0.zip
macOS Binary (x86_64) methylclock_1.10.0.tgz
macOS Binary (arm64) methylclock_1.10.0.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/
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