MammalMethylClock R package: software for DNA methylation-based epigenetic clocks in mammals.

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Defined as multivariate regression models, these DNA methylation-based biomarkers of age or mortality risk are useful in species conservation efforts and in preclinical studies.\nRESULTS: We present an R package called MammalMethylClock for the construction, assessment, and application of epigenetic clocks in different mammalian species. The R package includes the utility for implementing pre-existing mammalian clocks from the Mammalian Methylation Consortium.\nAVAILABILITY AND IMPLEMENTATION: The source code and documentation manual for MammalMethylClock, and clock coefficient .csv files that are included within this software package, can be found on Zenodo at https://doi.org/10.5281/zenodo.10971037.", "claims": [{"id": "claim-method", "statement": "Central to the construction of most epigenetic clocks is a sparse, penalized regression method such as elastic net regression or LASSO (Tibshirani 1996, Zou and Hastie 2005).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38656974", "locator": "sections[6] \"3.1 Epigenetic clocks as penalized regression models\" paragraph 4", "quote": "Central to the construction of most epigenetic clocks is a sparse, penalized regression method such as elastic net regression or LASSO (Tibshirani 1996, Zou and Hastie 2005)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Supplementary data are available at Bioinformatics online.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38656974", "locator": "sections[14] \"Supplementary data\" paragraph 2", "quote": "Supplementary data are available at Bioinformatics online."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38656974"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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