Clock glossary

Clock glossary#

This is a table with the metadata of the clocks available at the moment on pyaging, including additional implementation notes for each clock:

Clock name	Data type	Species	Year	Approved by author(s)	DOI	Miscellaneous notes	Preprocess	Postprocess	Reference values
altumage	methylation	Homo sapiens	2022	✅	https://doi.org/10.1038/s41514-022-00085-y		scale		True
bitage	transcriptomics	C elegans	2021	✅	https://doi.org/10.1111/acel.13320		binarize
camilloh3k27ac	histone mark	Homo sapiens	2023	✅	https://doi.org/10.1101/2023.08.21.554165
camilloh3k27me3	histone mark	Homo sapiens	2023	✅	https://doi.org/10.1101/2023.08.21.554165
camilloh3k36me3	histone mark	Homo sapiens	2023	✅	https://doi.org/10.1101/2023.08.21.554165
camilloh3k4me1	histone mark	Homo sapiens	2023	✅	https://doi.org/10.1101/2023.08.21.554165
camilloh3k4me3	histone mark	Homo sapiens	2023	✅	https://doi.org/10.1101/2023.08.21.554165
camilloh3k9ac	histone mark	Homo sapiens	2023	✅	https://doi.org/10.1101/2023.08.21.554165
camilloh3k9me3	histone mark	Homo sapiens	2023	✅	https://doi.org/10.1101/2023.08.21.554165
camillopanhistone	histone mark	Homo sapiens	2023	✅	https://doi.org/10.1101/2023.08.21.554165
cpgptgrimage3	methylation	Homo sapiens	2025	✅	https://doi.org/10.1101/2024.10.24.619766		scale	cox_to_years
cpgptpcgrimage3	methylation	Homo sapiens	2025	✅	https://doi.org/10.1101/2024.10.24.619766		scale	cox_to_years
dunedinpace	methylation	Homo sapiens	2022	✅	https://doi.org/10.7554/eLife.73420	This model is for research purposes only. Commercial users should contact exclusive DunedinPACE licensee TruDiagnosticTM. The automatic failure if fewer than 80% of the CpG probes are available is not implemented and left to the user’s discretion.	quantile_normalization_with_gold_standard		True
han	methylation	Homo sapiens	2020	✅	https://doi.org/10.1186/s12915-020-00807-2			anti_log_linear
knight	methylation	Homo sapiens	2016	✅	https://doi.org/10.1186/s13059-016-1068-z				True
leecontrol	methylation	Homo sapiens	2019	✅	https://doi.org/10.18632/aging.102049
leerefinedrobust	methylation	Homo sapiens	2019	✅	https://doi.org/10.18632/aging.102049
leerobust	methylation	Homo sapiens	2019	✅	https://doi.org/10.18632/aging.102049
pasta	transcriptomics	Homo sapiens	2025	✅	https://doi.org/10.1101/2025.06.04.657785	Rank-normalized transcriptomic clock.	median_fill_and_rank_normalization	scale_and_shift	True
pastamouse	transcriptomics	Mus musculus	2025	✅	https://doi.org/10.1101/2025.06.04.657785	Rank-normalized Pasta clock using mouse one-to-one ortholog genes when available.	median_fill_and_rank_normalization	scale_and_shift	True
pipekelasticnet	methylation	Homo sapiens	2022	✅	https://doi.org/10.1007/s10910-022-01381-4			anti_log_linear
pipekfilteredh	methylation	Homo sapiens	2022	✅	https://doi.org/10.1007/s10910-022-01381-4			anti_log_linear
pipekretrainedh	methylation	Homo sapiens	2022	✅	https://doi.org/10.1007/s10910-022-01381-4			anti_log_linear
reg	transcriptomics	Homo sapiens	2025	✅	https://doi.org/10.1101/2025.06.04.657785	Rank-normalized transcriptomic clock (Age in years).	median_fill_and_rank_normalization	add_constant	True
stemtoc	methylation	Homo sapiens	2024	✅	https://doi.org/10.1038/s41467-024-48649-8	The reference values are simply -1 for the algorithm to ignore them.	0.95 quantile		True
stoch	methylation	Homo sapiens	2024	✅	https://doi.org/10.1038/s43587-024-00600-8
stocp	methylation	Homo sapiens	2024	✅	https://doi.org/10.1038/s43587-024-00600-8
stocz	methylation	Homo sapiens	2024	✅	https://doi.org/10.1038/s43587-024-00600-8
thompson	methylation	Mus musculus	2018	✅	https://doi.org/10.18632/aging.101590
abec	methylation	Homo sapiens	2020	⌛	https://doi.org/10.1186/s12864-020-07168-8
cabec	methylation	Homo sapiens	2020	⌛	https://doi.org/10.1186/s12864-020-07168-8
deconvolutebloodepicbcell	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-025-00987-y	Estimated proportion of b_cell from EPIC reference.	fill_with_reference_means		True
deconvolutebloodepiccd4tcell	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-025-00987-y	Estimated proportion of cd4_t_cell from EPIC reference.	fill_with_reference_means		True
deconvolutebloodepiccd8tcell	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-025-00987-y	Estimated proportion of cd8_t_cell from EPIC reference.	fill_with_reference_means		True
deconvolutebloodepicmonocyte	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-025-00987-y	Estimated proportion of monocyte from EPIC reference.	fill_with_reference_means		True
deconvolutebloodepicneutrophil	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-025-00987-y	Estimated proportion of neutrophil from EPIC reference.	fill_with_reference_means		True
deconvolutebloodepicnkcell	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-025-00987-y	Estimated proportion of nk_cell from EPIC reference.	fill_with_reference_means		True
dnamfitage	methylation	Homo sapiens	2023	⌛	https://doi.org/10.18632/aging.204538	Reference values is mean between male and female training medians			True
dnamfitagegaitf	methylation	Homo sapiens	2023	⌛	https://doi.org/10.18632/aging.204538	Reference values is mean between male and female training medians			True
dnamfitagegaitm	methylation	Homo sapiens	2023	⌛	https://doi.org/10.18632/aging.204538	Reference values is mean between male and female training medians			True
dnamfitagegripf	methylation	Homo sapiens	2023	⌛	https://doi.org/10.18632/aging.204538	Reference values is mean between male and female training medians			True
dnamfitagegripm	methylation	Homo sapiens	2023	⌛	https://doi.org/10.18632/aging.204538	Reference values is mean between male and female training medians			True
dnamfitagevo2max	methylation	Homo sapiens	2023	⌛	https://doi.org/10.18632/aging.204538	Reference values is mean between male and female training medians			True
dnamic	methylation	Homo sapiens	2025	⌛	https://doi.org/10.1038/s43587-025-00883-5
dnamphenoage	methylation	Homo sapiens	2018	⌛	https://doi.org/10.18632%2Faging.101414
dnamtl	methylation	Homo sapiens	2019	⌛	https://doi.org/10.18632/aging.102173
eabec	methylation	Homo sapiens	2020	⌛	https://doi.org/10.1186/s12864-020-07168-8
encen100	methylation	Homo sapiens	2023	⌛	https://doi.org/10.1007/s11357-023-00731-7
encen40	methylation	Homo sapiens	2023	⌛	https://doi.org/10.1007/s11357-023-00731-7
ensembleagestatic	methylation	Mus musculus	2025	⌛	https://doi.org/10.1007/s11357-025-01808-1
ensembleagestatictop	methylation	Mus musculus	2025	⌛	https://doi.org/10.1007/s11357-025-01808-1
epitoc1	methylation	Homo sapiens	2016	⌛	https://doi.org/10.1186/s13059-016-1064-3	The reference values are simply -1 for the algorithm to ignore them.	mean		True
epitoc2	methylation	Homo sapiens	2020	⌛	https://doi.org/10.1186/s13073-020-00752-3	Stem cell division rate estimate using EpiTOC2.	nan_to_zero		True
grimage	methylation	Homo sapiens	2019	⌛	https://doi.org/10.18632/aging.101684			cox_to_years	True
grimage2	methylation	Homo sapiens	2022	⌛	https://doi.org/10.18632/aging.204434			cox_to_years	True
grimage2adm	methylation	Homo sapiens	2022	⌛	https://doi.org/10.18632/aging.204434			cox_to_years	True
grimage2b2m	methylation	Homo sapiens	2022	⌛	https://doi.org/10.18632/aging.204434			cox_to_years	True
grimage2cystatinc	methylation	Homo sapiens	2022	⌛	https://doi.org/10.18632/aging.204434			cox_to_years	True
grimage2gdf15	methylation	Homo sapiens	2022	⌛	https://doi.org/10.18632/aging.204434			cox_to_years	True
grimage2leptin	methylation	Homo sapiens	2022	⌛	https://doi.org/10.18632/aging.204434			cox_to_years	True
grimage2loga1c	methylation	Homo sapiens	2022	⌛	https://doi.org/10.18632/aging.204434			cox_to_years	True
grimage2logcrp	methylation	Homo sapiens	2022	⌛	https://doi.org/10.18632/aging.204434			cox_to_years	True
grimage2packyrs	methylation	Homo sapiens	2022	⌛	https://doi.org/10.18632/aging.204434			cox_to_years	True
grimage2pai1	methylation	Homo sapiens	2022	⌛	https://doi.org/10.18632/aging.204434				True
grimage2timp1	methylation	Homo sapiens	2022	⌛	https://doi.org/10.18632/aging.204434			cox_to_years	True
hannum	methylation	Homo sapiens	2013	⌛	https://doi.org/10.1016/j.molcel.2012.10.016
horvath2013	methylation	Homo sapiens	2013	⌛	https://doi.org/10.1186/gb-2013-14-10-r115			anti_log_linear	True
hrsinchphenoage	methylation	Homo sapiens	2022	⌛	https://doi.org/10.1038/s43587-022-00248-2
hypoclock	methylation	Homo sapiens	2018	⌛	https://doi.org/10.1038/s41588-018-0073-4	HypoClock score is 1 - mean beta across 678 solo-WCGW CpGs; reference values are -1 to ignore missing.	mean	one_minus	True
intrinclock	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s42003-024-06609-4			anti_log_linear
lin	methylation	Homo sapiens	2016	⌛	https://doi.org/10.18632/aging.100908
mammalian1	methylation	multi	2023	⌛	https://doi.org/10.1038/s43587-023-00462-6			anti_logp2
mammalian2	methylation	multi	2023	⌛	https://doi.org/10.1038/s43587-023-00462-6			mammalian2	True
mammalian3	methylation	multi	2023	⌛	https://doi.org/10.1038/s43587-023-00462-6			mammalian3	True
mammalianblood2	methylation	multi	2023	⌛	https://doi.org/10.1038/s43587-023-00462-6			mammalian2	True
mammalianblood3	methylation	multi	2023	⌛	https://doi.org/10.1038/s43587-023-00462-6			mammalian3	True
mammalianfemale	methylation	multi	2023	⌛	https://doi.org/10.1101/2023.11.02.565286			sigmoid
mammalianlifespan	methylation	multi	2023	⌛	https://doi.org/10.1101/2023.11.02.565286			anti_log	True
mammalianskin2	methylation	multi	2023	⌛	https://doi.org/10.1038/s43587-023-00462-6			mammalian2	True
mammalianskin3	methylation	multi	2023	⌛	https://doi.org/10.1038/s43587-023-00462-6			mammalian3	True
mccartneybmi	methylation	Homo sapiens	2018	⌛	https://doi.org/10.1186/s13059-018-1514-1	DNAm score for BMI; logistic transform.		sigmoid
mccartneybodyfat	methylation	Homo sapiens	2018	⌛	https://doi.org/10.1186/s13059-018-1514-1	DNAm score for body fat percentage; logistic transform.		sigmoid
mccartneyeducation	methylation	Homo sapiens	2018	⌛	https://doi.org/10.1186/s13059-018-1514-1	DNAm score for educational attainment; logistic transform.		sigmoid
mccartneyhdlcholesterol	methylation	Homo sapiens	2018	⌛	https://doi.org/10.1186/s13059-018-1514-1	DNAm score for HDL cholesterol; logistic transform.		sigmoid
mccartneyldlcholesterol	methylation	Homo sapiens	2018	⌛	https://doi.org/10.1186/s13059-018-1514-1	DNAm score for LDL with remnant cholesterol; logistic transform.		sigmoid
mccartneysmoking	methylation	Homo sapiens	2018	⌛	https://doi.org/10.1186/s13059-018-1514-1	Linear CpG score; higher values indicate smoking exposure.
mccartneytotalcholesterol	methylation	Homo sapiens	2018	⌛	https://doi.org/10.1186/s13059-018-1514-1	DNAm score for total cholesterol; logistic transform.		sigmoid
meer	methylation	Mus musculus	2018	⌛	https://doi.org/10.7554/eLife.40675
ocampoatac1	atac	Homo sapiens	2023	⌛	https://doi.org/10.1007/s11357-023-00986-0		tpm_norm_log1p
ocampoatac2	atac	Homo sapiens	2023	⌛	https://doi.org/10.1007/s11357-023-00986-0		tpm_norm_log1p
pcdnamtl	methylation	Homo sapiens	2022	⌛	https://doi.org/10.1038/s43587-022-00248-2				True
pcgrimage	methylation	Homo sapiens	2022	⌛	https://doi.org/10.1038/s43587-022-00248-2				True
pchannum	methylation	Homo sapiens	2022	⌛	https://doi.org/10.1038/s43587-022-00248-2				True
pchorvath2013	methylation	Homo sapiens	2022	⌛	https://doi.org/10.1038/s43587-022-00248-2			anti_log_linear	True
pcphenoage	methylation	Homo sapiens	2022	⌛	https://doi.org/10.1038/s43587-022-00248-2				True
pcskinandblood	methylation	Homo sapiens	2022	⌛	https://doi.org/10.1038/s43587-022-00248-2			anti_log_linear	True
pedbe	methylation	Homo sapiens	2019	⌛	https://doi.org/10.1073/pnas.1820843116			anti_log_linear
petkovich	methylation	Mus musculus	2017	⌛	https://doi.org/10.1016/j.cmet.2017.03.016			petkovich
phenoage	blood chemistry	Homo sapiens	2018	⌛	https://doi.org/10.18632%2Faging.101414			mortality_to_phenoage
replitali	methylation	Homo sapiens	2022	⌛	https://doi.org/10.1038/s41467-022-34268-8
retroelementagev1	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1111/acel.14288
retroelementagev2	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1111/acel.14288
skinandblood	methylation	Homo sapiens	2018	⌛	https://doi.org/10.18632/aging.101508			anti_log_linear
stubbs	methylation	Mus musculus	2017	⌛	https://doi.org/10.1186/s13059-017-1203-5		quantile_normalization_and_scale_with_gold_standard	stubbs	True
systemsage	methylation	Homo sapiens	2025	⌛	https://doi.org/10.1038/s43587-025-00958-3				True
systemsageblood	methylation	Homo sapiens	2025	⌛	https://doi.org/10.1038/s43587-025-00958-3				True
systemsagebrain	methylation	Homo sapiens	2025	⌛	https://doi.org/10.1038/s43587-025-00958-3				True
systemsageheart	methylation	Homo sapiens	2025	⌛	https://doi.org/10.1038/s43587-025-00958-3				True
systemsagehormone	methylation	Homo sapiens	2025	⌛	https://doi.org/10.1038/s43587-025-00958-3				True
systemsageimmune	methylation	Homo sapiens	2025	⌛	https://doi.org/10.1038/s43587-025-00958-3				True
systemsageinflammation	methylation	Homo sapiens	2025	⌛	https://doi.org/10.1038/s43587-025-00958-3				True
systemsagekidney	methylation	Homo sapiens	2025	⌛	https://doi.org/10.1038/s43587-025-00958-3				True
systemsageliver	methylation	Homo sapiens	2025	⌛	https://doi.org/10.1038/s43587-025-00958-3				True
systemsagelung	methylation	Homo sapiens	2025	⌛	https://doi.org/10.1038/s43587-025-00958-3				True
systemsagemetabolic	methylation	Homo sapiens	2025	⌛	https://doi.org/10.1038/s43587-025-00958-3				True
systemsagemusculoskeletal	methylation	Homo sapiens	2025	⌛	https://doi.org/10.1038/s43587-025-00958-3				True
twelvecelldeconvolutebloodepicbas	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-025-00987-y	Estimated proportion of Bas from 12-cell EPIC reference.	fill_with_reference_means		True
twelvecelldeconvolutebloodepicbmem	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-025-00987-y	Estimated proportion of Bmem from 12-cell EPIC reference.	fill_with_reference_means		True
twelvecelldeconvolutebloodepicbnv	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-025-00987-y	Estimated proportion of Bnv from 12-cell EPIC reference.	fill_with_reference_means		True
twelvecelldeconvolutebloodepiccd4mem	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-025-00987-y	Estimated proportion of CD4mem from 12-cell EPIC reference.	fill_with_reference_means		True
twelvecelldeconvolutebloodepiccd4nv	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-025-00987-y	Estimated proportion of CD4nv from 12-cell EPIC reference.	fill_with_reference_means		True
twelvecelldeconvolutebloodepiccd8mem	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-025-00987-y	Estimated proportion of CD8mem from 12-cell EPIC reference.	fill_with_reference_means		True
twelvecelldeconvolutebloodepiccd8nv	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-025-00987-y	Estimated proportion of CD8nv from 12-cell EPIC reference.	fill_with_reference_means		True
twelvecelldeconvolutebloodepiceos	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-025-00987-y	Estimated proportion of Eos from 12-cell EPIC reference.	fill_with_reference_means		True
twelvecelldeconvolutebloodepicmono	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-025-00987-y	Estimated proportion of Mono from 12-cell EPIC reference.	fill_with_reference_means		True
twelvecelldeconvolutebloodepicneu	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-025-00987-y	Estimated proportion of Neu from 12-cell EPIC reference.	fill_with_reference_means		True
twelvecelldeconvolutebloodepicnk	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-025-00987-y	Estimated proportion of NK from 12-cell EPIC reference.	fill_with_reference_means		True
twelvecelldeconvolutebloodepictreg	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-025-00987-y	Estimated proportion of Treg from 12-cell EPIC reference.	fill_with_reference_means		True
xchrom	methylation	Homo sapiens	2021	⌛	https://doi.org/10.1186/s12864-021-07675-2	X-chrom score: positive ~ more X (female/XX/XXY), negative ~ fewer X (male/XO).	sex_estimation_autosomal_zscore		True
ychrom	methylation	Homo sapiens	2021	⌛	https://doi.org/10.1186/s12864-021-07675-2	Y-chrom score: positive ~ Y present (male/XXY), negative ~ Y absent (female/XO).	sex_estimation_autosomal_zscore		True
yingadaptage	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-023-00557-0
yingcausage	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-023-00557-0
yingdamage	methylation	Homo sapiens	2024	⌛	https://doi.org/10.1038/s43587-023-00557-0
zhangblup	methylation	Homo sapiens	2019	⌛	https://doi.org/10.1186/s13073-019-0667-1		scale_row		True
zhangen	methylation	Homo sapiens	2019	⌛	https://doi.org/10.1186/s13073-019-0667-1		scale_row		True
zhangmortality	methylation	Homo sapiens	2017	⌛	https://doi.org/10.1038/ncomms14617