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>

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

Installation

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

if (!requireNamespace("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

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