# Mammalian Methylation Consortium Github Page

This page contains all the annotation and tools generated by Mammalian Methylation Consortium to analyze generated data using Mammal40k and Mammal320 arrays:

Here are the summary of the content:  
1- Genome coordinates for different species  
2- R code for alignment and annotation  
3- The array manifest  
4- Details on probe design  
5- R code for Sesame normalization  
6- R code for universal pan-mammalian epigenetic clocks, universal blood epigenetic clocks, universal skin epigenetic clocks, adaptions to Illumina 450k/EPIC array, and an example dataset  
7- Various tissue, sex, and species predictors for mammalian species  
8- Codes used for Mammalian Network Analysis in the paper, Haghani et al. DNA Methylation Networks Underlying Mammalian Traits, Science Magazine, 2023.  
9- **EnsembleAge R Package**: Complete R package for automated multi-platform epigenetic age prediction with ensemble methods (Human, Mammal40k, Mammal320k arrays). Features automatic platform detection, data preprocessing, and 110+ individual clocks including EnsembleAge Static/Dynamic, Universal clocks, and original mammalian clocks. Installation: `devtools::install_github('ahaghani/EnsembleAge')` - one-line prediction with `predictEnsemble(data, samples)`. Published methodology provides enhanced accuracy through ensemble approaches combining multiple clock families for robust age predictions across species and tissues.

Key references on Mammalian Methylation Array:

Details on the array development:  
Arneson, A., Haghani, A., Thompson, M. J., Pellegrini, M., Kwon, S. B., Vu, H., Maciejewski, E., Yao, M., Li, C. Z., Lu, A. T., Morselli, M., Rubbi, L., Barnes, B., Hansen, K. D., Zhou, W., Breeze, C. E., Ernst, J., & Horvath, S. (2022). A mammalian methylation array for profiling methylation levels at conserved sequences. Nat Commun, 13(1), 783. https://doi.org/10.1038/s41467-022-28355-z 

Mammalian Methylation Dataset and a cross species meta analysis:  
Haghani, A., Li, C. Z., Robeck, T. R., Zhang, J., Lu, A. T., Ablaeva, J., Acosta-Rodriguez, V. A., Adams, D. M., Alagaili, A. N., Almunia, J., Aloysius, A., Amor, N. M. S., Ardehali, R., Arneson, A., Baker, C. S., Banks, G., Belov, K., Bennett, N. C., Black, P., . . . Horvath, S. (2023). DNA methylation networks underlying mammalian traits. Science, 381(6658), eabq5693. https://doi.org/10.1126/science.abq5693 

A paper on the universal epigenetic clocks in mammals:  
Lu, A. T., Fei, Z., Haghani, A., Robeck, T. R., Zoller, J. A., Li, C. Z., Lowe, R., Yan, Q., Zhang, J., Vu, H., Ablaeva, J., Acosta-Rodriguez, V. A., Adams, D. M., Almunia, J., Aloysius, A., Ardehali, R., Arneson, A., Baker, C. S., Banks, G., . . . Horvath, S. (2023). Universal DNA methylation age across mammalian tissues. Nat Aging. https://doi.org/10.1038/s43587-023-00462-6 

EnsembleAge package for multi-platform epigenetic age prediction:  
Haghani, A., Lu, A.T., Yan, Q. et al. EnsembleAge: enhancing epigenetic age assessment with a multi-clock framework. GeroScience (2025). DOI: [10.1007/s11357-025-01808-1](https://doi.org/10.1007/s11357-025-01808-1)

## EnsembleAge R Package

**Latest Addition:** Complete R package for multi-platform epigenetic age prediction using ensemble methods.

- **Repository**: [EnsembleAge](./EnsembleAge/)
- **Installation**: `devtools::install_github('ahaghani/EnsembleAge', ref='v0.99.1')`
- **Platforms**: Human, Mammal40k, Mammal320k arrays (automatic detection)
- **Publication**: Haghani, A., Lu, A.T., Yan, Q. et al. EnsembleAge: enhancing epigenetic age assessment with a multi-clock framework. GeroScience (2025). DOI: [10.1007/s11357-025-01808-1](https://doi.org/10.1007/s11357-025-01808-1)
- **Release DOI**: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.16814673.svg)](https://doi.org/10.5281/zenodo.16814673)