methylclock
This is the development version of methylclock; for the stable release version, see methylclock.
Methylclock - DNA methylation-based clocks
Bioconductor version: Development (3.24)
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("methylclock")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiologicalQuestion, DNAMethylation, Normalization, Preprocessing, Software, StatisticalMethod |
| Version | 1.19.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (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_1.19.0.tar.gz |
| Windows Binary (x86_64) | methylclock_1.19.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | methylclock_1.19.0.tgz |
| macOS Binary (sonoma-arm64) | methylclock_1.19.0.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 |