EpigeneticAgePipeline: An R Package for Comprehensive Assessment of Epigenetic Age Metrics From Methylation Microarrays

Apr 2, 2026Bioinformatics and biology insights

EpigeneticAgePipeline: A Tool for Measuring Biological Age Using DNA Methylation Data

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Longevity & Aging on OpenScience ↗PubMed ↗DOI ↗OA ↗

Abstract

EpigeneticAgePipeline is an R package designed for estimating biological age using multiple epigenetic clocks.

Epigenetic age is assessed through changes in DNA methylation patterns associated with aging.
The package can estimate various epigenetic age metrics, including Horvath, Hannum, and GrimAge.
Quality control measures include sample and probe-level filtering and intensity checks.
The pipeline supports several Illumina methylation microarrays for comprehensive analysis.
Validation with GEO data set GSE237561 confirmed the accuracy of the pipeline.
Future updates are planned to incorporate new epigenetic age measures as they emerge.

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Epigenetic age is a biological age estimate based on nuclear DNA methylation patterns. Epigenetic clocks measure biological age by analyzing predictable changes in DNA methylation sites associated with aging. This study introduces EpigeneticAgePipeline, an R package that streamlines the estimation of epigenetic age metrics including Horvath, Horvath skin and blood, Hannum, PhenoAge/Levine, GrimAge (V1 and V2), and DunedinPACE plus additional acceleration metrics based on all other clocks. Quality control includes detection-value filtering (sample- and probe-level), bead-count thresholds, and Illumina quality control intensity checks. EpigeneticAgePipeline supports Illumina Infinium methylation microarrays (HumanMethylation27, HumanMethylation450, HumanMethylationEPIC/EPICv2, and Human Methylation Screening Array). It offers functionalities including data preprocessing, normalization, cell count imputation, residual generation accounting for principal components and batch effects, and extensive visualizations for improved interpretability. Validation was performed using GEO data set GSE237561, confirming the accuracy of the pipeline. EpigeneticAgePipeline provides an integrated workflow from raw data to advanced statistical analyses and visualizations, improving usability over existing tools. In addition to the traditional clocks mentioned, the package also integrates a set of additional epigenetic age clocks (PedBE, Wu, TL, BLUP, and EN). Future updates will include emerging epigenetic age measures to maintain relevance in this evolving field. P

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EpigeneticAgePipeline: An R Package for Comprehensive Assessment of Epigenetic Age Metrics From Methylation Microarrays

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