Package: methylclock
Type: Package
Title: Chronological, Gestational and Biological DNAm Age Estimation
        with Methylation-Based Clocks
Version: 1.99.1
Date: 2026-09-10
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")),
    person("Carlos", "Ruiz-Arenas", email = "carlos.ruiz@isglobal.org", role = "aut"))
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
git_url: https://git.bioconductor.org/packages/methylclock
git_branch: devel
git_last_commit: cb06285
git_last_commit_date: 2026-09-10
Repository: Bioconductor 3.24
Date/Publication: 2026-09-10
NeedsCompilation: yes
Packaged: 2026-09-10 22:50:18 UTC; biocbuild
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>),
  Carlos Ruiz-Arenas [aut]
Maintainer: Dolors Pelegri-Siso <dolors.pelegri@isglobal.org>
