Package: methylclock
Type: Package
Title: Chronological, Gestational and Biological DNAm Age Estimation
        with Methylation-Based Clocks
Version: 1.99.2
Date: 2026-09-14
Authors@R: c(
    person("Dolors", "Pelegri-Siso", email = "dolors.pelegri@isglobal.org",
           role = c("aut", "cre"), comment = c(ORCID = "0000-0002-5993-3003")),
    person("Juan R.", "Gonzalez", email = "juanr.gonzalez@isglobal.org",
           role = "aut", comment = c(ORCID = "0000-0003-3267-2146")))
Description: Estimates chronological, gestational and biological DNA
        methylation (DNAm) age, trait scores and epigenetic age
        acceleration from methylation beta values. Implements 44
        published clocks, selectable by name, family or array platform:
        chronological (Horvath, Hannum, BNN, skin+blood, PedBE, Wu,
        AltumAge and others, including the cross-platform Garma clock
        native to EPICv2), gestational (Knight, Bohlin, Mayne, Lee,
        NEOage), phenotypic and pace-of-aging (Levine, DunedinPACE),
        telomere length, mitotic counters (epiTOC1/epiTOC2, HypoClock,
        stemTOC, RepliTali), causal (CausAge, DamAge, AdaptAge) and
        trait EpiScores. Accepts matrices, data frames, Bioconductor
        containers or HDF5 files, computing block-wise out-of-core
        through BigDataStatMeth when the data exceed memory. Provides
        configurable missing-value imputation (mean, reference or KNN),
        cell-type deconvolution, intrinsic and extrinsic epigenetic age
        acceleration (IEAA, EEAA), quality-control reports and plotting
        functions.
biocViews: DNAMethylation, BiologicalQuestion, Preprocessing,
        StatisticalMethod, Normalization
License: MIT + file LICENSE
SystemRequirements: GNU make, C++17
Depends: R (>= 4.3.0)
Imports: utils, stats, preprocessCore, Rcpp, BigDataStatMeth,
        ExperimentHub, ggplot2, rlang, quadprog
LinkingTo: Rcpp, RcppEigen, Rhdf5lib, BigDataStatMeth, BH
Suggests: testthat (>= 3.0.0), digest, impute, knitr, rmarkdown,
        BiocStyle, kableExtra, minfi, Biobase, SummarizedExperiment
Encoding: UTF-8
URL: https://github.com/isglobal-brge/methylclock
BugReports: https://github.com/isglobal-brge/methylclock/issues
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/pak/sysreqs: make libicu-dev libpng-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-09-14 11:29:34 UTC
RemoteUrl: https://github.com/bioc/methylclock
RemoteRef: HEAD
RemoteSha: 30be0284066fda7d2f81ec4bf427da56f0f89d1b
NeedsCompilation: yes
Packaged: 2026-10-14 11:36:31 UTC; root
Author: Dolors Pelegri-Siso [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5993-3003>),
  Juan R. Gonzalez [aut] (ORCID: <https://orcid.org/0000-0003-3267-2146>)
Maintainer: Dolors Pelegri-Siso <dolors.pelegri@isglobal.org>