├── .cursor └── rules │ └── best-practices.mdc ├── .github └── workflows │ ├── build.yml │ ├── publish.yml │ ├── release.yml │ └── test.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── Makefile ├── README.md ├── clocks ├── notebooks │ ├── abec.ipynb │ ├── altumage.ipynb │ ├── bitage.ipynb │ ├── cabec.ipynb │ ├── camilloh3k27ac.ipynb │ ├── camilloh3k27me3.ipynb │ ├── camilloh3k36me3.ipynb │ ├── camilloh3k4me1.ipynb │ ├── camilloh3k4me3.ipynb │ ├── camilloh3k9ac.ipynb │ ├── camilloh3k9me3.ipynb │ ├── camillopanhistone.ipynb │ ├── cpgptgrimage3.ipynb │ ├── cpgptpcgrimage3.ipynb │ ├── deconvolutebloodepicbcell.ipynb │ ├── deconvolutebloodepiccd4tcell.ipynb │ ├── deconvolutebloodepiccd8tcell.ipynb │ ├── deconvolutebloodepicmonocyte.ipynb │ ├── deconvolutebloodepicneutrophil.ipynb │ ├── deconvolutebloodepicnkcell.ipynb │ ├── dnamfitage.ipynb │ ├── dnamfitagegaitf.ipynb │ ├── dnamfitagegaitm.ipynb │ ├── dnamfitagegripf.ipynb │ ├── dnamfitagegripm.ipynb │ ├── dnamfitagevo2max.ipynb │ ├── dnamic.ipynb │ ├── dnamphenoage.ipynb │ ├── dnamtl.ipynb │ ├── dunedinpace.ipynb │ ├── eabec.ipynb │ ├── encen100.ipynb │ ├── encen40.ipynb │ ├── ensembleagestatic.ipynb │ ├── ensembleagestatictop.ipynb │ ├── epitoc1.ipynb │ ├── epitoc2.ipynb │ ├── grimage.ipynb │ ├── grimage2.ipynb │ ├── grimage2adm.ipynb │ ├── grimage2b2m.ipynb │ ├── grimage2cystatinc.ipynb │ ├── grimage2gdf15.ipynb │ ├── grimage2leptin.ipynb │ ├── grimage2loga1c.ipynb │ ├── grimage2logcrp.ipynb │ ├── grimage2packyrs.ipynb │ ├── grimage2pai1.ipynb │ ├── grimage2timp1.ipynb │ ├── han.ipynb │ ├── hannum.ipynb │ ├── horvath2013.ipynb │ ├── hrsinchphenoage.ipynb │ ├── intrinclock.ipynb │ ├── knight.ipynb │ ├── leecontrol.ipynb │ ├── leerefinedrobust.ipynb │ ├── leerobust.ipynb │ ├── lin.ipynb │ ├── mammalian1.ipynb │ ├── mammalian2.ipynb │ ├── mammalian3.ipynb │ ├── mammalianblood2.ipynb │ ├── mammalianblood3.ipynb │ ├── mammalianfemale.ipynb │ ├── mammalianlifespan.ipynb │ ├── mammalianskin2.ipynb │ ├── mammalianskin3.ipynb │ ├── mccartneybmi.ipynb │ ├── mccartneybodyfat.ipynb │ ├── mccartneyeducation.ipynb │ ├── mccartneyhdlcholesterol.ipynb │ ├── mccartneyldlcholesterol.ipynb │ ├── mccartneysmoking.ipynb │ ├── mccartneytotalcholesterol.ipynb │ ├── meer.ipynb │ ├── ocampoatac1.ipynb │ ├── ocampoatac2.ipynb │ ├── pasta.ipynb │ ├── pastamouse.ipynb │ ├── pcdnamtl.ipynb │ ├── pcgrimage.ipynb │ ├── pchannum.ipynb │ ├── pchorvath2013.ipynb │ ├── pcphenoage.ipynb │ ├── pcskinandblood.ipynb │ ├── pedbe.ipynb │ ├── petkovich.ipynb │ ├── phenoage.ipynb │ ├── pipekelasticnet.ipynb │ ├── pipekfilteredh.ipynb │ ├── pipekretrainedh.ipynb │ ├── reg.ipynb │ ├── replitali.ipynb │ ├── retroelementagev1.ipynb │ ├── retroelementagev2.ipynb │ ├── skinandblood.ipynb │ ├── stemtoc.ipynb │ ├── stoch.ipynb │ ├── stocp.ipynb │ ├── stocz.ipynb │ ├── stubbs.ipynb │ ├── systemsage.ipynb │ ├── systemsageblood.ipynb │ ├── systemsagebrain.ipynb │ ├── systemsageheart.ipynb │ ├── systemsagehormone.ipynb │ ├── systemsageimmune.ipynb │ ├── systemsageinflammation.ipynb │ ├── systemsagekidney.ipynb │ ├── systemsageliver.ipynb │ ├── systemsagelung.ipynb │ ├── systemsagemetabolic.ipynb │ ├── systemsagemusculoskeletal.ipynb │ ├── template.ipynb │ ├── thompson.ipynb │ ├── twelvecelldeconvolutebloodepicbas.ipynb │ ├── twelvecelldeconvolutebloodepicbmem.ipynb │ ├── twelvecelldeconvolutebloodepicbnv.ipynb │ ├── twelvecelldeconvolutebloodepiccd4mem.ipynb │ ├── twelvecelldeconvolutebloodepiccd4nv.ipynb │ ├── twelvecelldeconvolutebloodepiccd8mem.ipynb │ ├── twelvecelldeconvolutebloodepiccd8nv.ipynb │ ├── twelvecelldeconvolutebloodepiceos.ipynb │ ├── twelvecelldeconvolutebloodepicmono.ipynb │ ├── twelvecelldeconvolutebloodepicneu.ipynb │ ├── twelvecelldeconvolutebloodepicnk.ipynb │ ├── twelvecelldeconvolutebloodepictreg.ipynb │ ├── xchrom.ipynb │ ├── ychrom.ipynb │ ├── yingadaptage.ipynb │ ├── yingcausage.ipynb │ ├── yingdamage.ipynb │ ├── zhangblup.ipynb │ ├── zhangen.ipynb │ └── zhangmortality.ipynb └── update_all_clocks.py ├── docs ├── Makefile ├── _static │ ├── clock_glossary.csv │ ├── clock_glossary.js │ ├── custom.css │ ├── logo.png │ ├── pyaging_graphical_abstract.pdf │ └── pyaging_graphical_abstract.png ├── environment.yml ├── make.bat └── source │ ├── _static │ └── clock_glossary.csv │ ├── clock_glossary.rst │ ├── clock_implementation.rst │ ├── clock_notebooks │ ├── abec.ipynb │ ├── altumage.ipynb │ ├── bitage.ipynb │ ├── cabec.ipynb │ ├── camilloh3k27ac.ipynb │ ├── camilloh3k27me3.ipynb │ ├── camilloh3k36me3.ipynb │ ├── camilloh3k4me1.ipynb │ ├── camilloh3k4me3.ipynb │ ├── camilloh3k9ac.ipynb │ ├── camilloh3k9me3.ipynb │ ├── camillopanhistone.ipynb │ ├── cpgptgrimage3.ipynb │ ├── cpgptpcgrimage3.ipynb │ ├── deconvolutebloodepicbcell.ipynb │ ├── deconvolutebloodepiccd4tcell.ipynb │ ├── deconvolutebloodepiccd8tcell.ipynb │ ├── deconvolutebloodepicmonocyte.ipynb │ ├── deconvolutebloodepicneutrophil.ipynb │ ├── deconvolutebloodepicnkcell.ipynb │ ├── dnamfitage.ipynb │ ├── dnamfitagegaitf.ipynb │ ├── dnamfitagegaitm.ipynb │ ├── dnamfitagegripf.ipynb │ ├── dnamfitagegripm.ipynb │ ├── dnamfitagevo2max.ipynb │ ├── dnamic.ipynb │ ├── dnamphenoage.ipynb │ ├── dnamtl.ipynb │ ├── dunedinpace.ipynb │ ├── eabec.ipynb │ ├── encen100.ipynb │ ├── encen40.ipynb │ ├── ensembleagestatic.ipynb │ ├── ensembleagestatictop.ipynb │ ├── epitoc1.ipynb │ ├── epitoc2.ipynb │ ├── grimage.ipynb │ ├── grimage2.ipynb │ ├── grimage2adm.ipynb │ ├── grimage2b2m.ipynb │ ├── grimage2cystatinc.ipynb │ ├── grimage2gdf15.ipynb │ ├── grimage2leptin.ipynb │ ├── grimage2loga1c.ipynb │ ├── grimage2logcrp.ipynb │ ├── grimage2packyrs.ipynb │ ├── grimage2pai1.ipynb │ ├── grimage2timp1.ipynb │ ├── han.ipynb │ ├── hannum.ipynb │ ├── horvath2013.ipynb │ ├── hrsinchphenoage.ipynb │ ├── intrinclock.ipynb │ ├── knight.ipynb │ ├── leecontrol.ipynb │ ├── leerefinedrobust.ipynb │ ├── leerobust.ipynb │ ├── lin.ipynb │ ├── mammalian1.ipynb │ ├── mammalian2.ipynb │ ├── mammalian3.ipynb │ ├── mammalianblood2.ipynb │ ├── mammalianblood3.ipynb │ ├── mammalianfemale.ipynb │ ├── mammalianlifespan.ipynb │ ├── mammalianskin2.ipynb │ ├── mammalianskin3.ipynb │ ├── mccartneybmi.ipynb │ ├── mccartneybodyfat.ipynb │ ├── mccartneyeducation.ipynb │ ├── mccartneyhdlcholesterol.ipynb │ ├── mccartneyldlcholesterol.ipynb │ ├── mccartneysmoking.ipynb │ ├── mccartneytotalcholesterol.ipynb │ ├── meer.ipynb │ ├── ocampoatac1.ipynb │ ├── ocampoatac2.ipynb │ ├── pasta.ipynb │ ├── pasta_mouse.ipynb │ ├── pastamouse.ipynb │ ├── pcdnamtl.ipynb │ ├── pcgrimage.ipynb │ ├── pchannum.ipynb │ ├── pchorvath2013.ipynb │ ├── pcphenoage.ipynb │ ├── pcskinandblood.ipynb │ ├── pedbe.ipynb │ ├── petkovich.ipynb │ ├── phenoage.ipynb │ ├── pipekelasticnet.ipynb │ ├── pipekfilteredh.ipynb │ ├── pipekretrainedh.ipynb │ ├── reg.ipynb │ ├── replitali.ipynb │ ├── retroelementagev1.ipynb │ ├── retroelementagev2.ipynb │ ├── skinandblood.ipynb │ ├── stemtoc.ipynb │ ├── stoch.ipynb │ ├── stocp.ipynb │ ├── stocz.ipynb │ ├── stubbs.ipynb │ ├── systemsage.ipynb │ ├── systemsageblood.ipynb │ ├── systemsagebrain.ipynb │ ├── systemsageheart.ipynb │ ├── systemsagehormone.ipynb │ ├── systemsageimmune.ipynb │ ├── systemsageinflammation.ipynb │ ├── systemsagekidney.ipynb │ ├── systemsageliver.ipynb │ ├── systemsagelung.ipynb │ ├── systemsagemetabolic.ipynb │ ├── systemsagemusculoskeletal.ipynb │ ├── template.ipynb │ ├── thompson.ipynb │ ├── twelvecelldeconvolutebloodepicbas.ipynb │ ├── twelvecelldeconvolutebloodepicbmem.ipynb │ ├── twelvecelldeconvolutebloodepicbnv.ipynb │ ├── twelvecelldeconvolutebloodepiccd4mem.ipynb │ ├── twelvecelldeconvolutebloodepiccd4nv.ipynb │ ├── twelvecelldeconvolutebloodepiccd8mem.ipynb │ ├── twelvecelldeconvolutebloodepiccd8nv.ipynb │ ├── twelvecelldeconvolutebloodepiceos.ipynb │ ├── twelvecelldeconvolutebloodepicmono.ipynb │ ├── twelvecelldeconvolutebloodepicneu.ipynb │ ├── twelvecelldeconvolutebloodepicnk.ipynb │ ├── twelvecelldeconvolutebloodepictreg.ipynb │ ├── xchrom.ipynb │ ├── ychrom.ipynb │ ├── yingadaptage.ipynb │ ├── yingcausage.ipynb │ ├── yingdamage.ipynb │ ├── zhangblup.ipynb │ ├── zhangen.ipynb │ └── zhangmortality.ipynb │ ├── conf.py │ ├── index.rst │ ├── installation.rst │ ├── make_clock_glossary.py │ ├── pyaging.data.rst │ ├── pyaging.models.rst │ ├── pyaging.predict.rst │ ├── pyaging.preprocess.rst │ ├── pyaging.rst │ ├── pyaging.utils.rst │ └── tutorials │ ├── tutorial_atacseq.ipynb │ ├── tutorial_bloodchemistry.ipynb │ ├── tutorial_cpgptgrimage3.ipynb │ ├── tutorial_dnam_illumina_human_array.ipynb │ ├── tutorial_dnam_illumina_mammalian_array.ipynb │ ├── tutorial_dnam_rrbs.ipynb │ ├── tutorial_histonemarkchipseq.ipynb │ ├── tutorial_rnaseq.ipynb │ └── tutorial_utils.ipynb ├── pyaging ├── __init__.py ├── data │ ├── __init__.py │ └── _data.py ├── logger │ ├── __init__.py │ └── _logger.py ├── models │ ├── __init__.py │ ├── _base_models.py │ └── _models.py ├── predict │ ├── __init__.py │ ├── _postprocessing.py │ ├── _pred.py │ ├── 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