Bump to v0.1.10

rsinghlab · Aug 12, 2024 · 8c5d4e6 · 8c5d4e6
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Showing 6 changed files with 1,818 additions and 2 deletions.
diff --git a/docs/_static/clock_glossary.csv b/docs/_static/clock_glossary.csv
@@ -28,9 +28,10 @@ encen40,methylation,Homo sapiens,2023,⌛,https://doi.org/10.1007/s11357-023-007
 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
 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
-hannum,methylation,Homo sapiens,2013,⌛,https://doi.org/10.1016/j.molcel.2012.10.016,,,,
+hannum,methylation,Homo sapiens,2024,⌛,https://doi.org/10.1111/acel.14288,,,,
 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,,,,
+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
@@ -54,6 +55,8 @@ pedbe,methylation,Homo sapiens,2019,⌛,https://doi.org/10.1073/pnas.1820843116,
 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
 yingadaptage,methylation,Homo sapiens,2024,⌛,https://doi.org/10.1038/s43587-023-00557-0,,,,

diff --git a/docs/source/clock_implementation.rst b/docs/source/clock_implementation.rst
@@ -29,6 +29,7 @@ The following collection of Jupyter Notebooks provides a comprehensive guide to
    clock_notebooks/hannum
    clock_notebooks/horvath2013
    clock_notebooks/hrsinchphenoage
+   clock_notebooks/intrinclock
    clock_notebooks/knight
    clock_notebooks/leecontrol
    clock_notebooks/leerefinedrobust
@@ -56,6 +57,8 @@ The following collection of Jupyter Notebooks provides a comprehensive guide to
    clock_notebooks/petkovich
    clock_notebooks/phenoage
    clock_notebooks/replitali
+   clock_notebooks/retroelementagev1
+   clock_notebooks/retroelementagev2
    clock_notebooks/skinandblood
    clock_notebooks/stemtoc
    clock_notebooks/stoch

diff --git a/docs/source/clock_notebooks/epitoc1.ipynb b/docs/source/clock_notebooks/epitoc1.ipynb
@@ -128,7 +128,7 @@
     "model.metadata[\"data_type\"] = 'methylation'\n",
     "model.metadata[\"species\"] = 'Homo sapiens'\n",
     "model.metadata[\"year\"] = 2016\n",
-    "model.metadata[\"approved_by_author\"] = '⌛'\n",
+    "model.metadata[\"approved_by_author\"] = '✅'\n",
     "model.metadata[\"citation\"] = \"Yang, Zhen, et al. \\\"Correlation of an epigenetic mitotic clock with cancer risk.\\\" Genome biology 17 (2016): 1-18.\"\n",
     "model.metadata[\"doi\"] = \"https://doi.org/10.1186/s13059-016-1064-3\"\n",
     "model.metadata[\"research_only\"] = None\n",