Sync stemtoc
Browse files- README.md +38 -0
- config.json +40 -0
- stemtoc.pt +3 -0
README.md
ADDED
|
@@ -0,0 +1,38 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
---
|
| 2 |
+
license: bsd-3-clause
|
| 3 |
+
library_name: pyaging
|
| 4 |
+
tags:
|
| 5 |
+
- pyaging
|
| 6 |
+
- aging-clock
|
| 7 |
+
- biology
|
| 8 |
+
- dna-methylation
|
| 9 |
+
---
|
| 10 |
+
|
| 11 |
+
# stemtoc
|
| 12 |
+
|
| 13 |
+
Relative mitotic-age counter based on the 95th percentile across 371 in-vivo-filtered mitotic CpGs.
|
| 14 |
+
|
| 15 |
+
| | |
|
| 16 |
+
|---|---|
|
| 17 |
+
| **Predicts** | mitotic age |
|
| 18 |
+
| **Species** | Homo sapiens |
|
| 19 |
+
| **Tissue** | multi-tissue, cultured human cells, whole blood |
|
| 20 |
+
| **Data type** | DNA methylation |
|
| 21 |
+
| **Model type** | 95th-percentile methylation aggregation |
|
| 22 |
+
| **Year** | 2024 |
|
| 23 |
+
|
| 24 |
+
## Use with pyaging
|
| 25 |
+
|
| 26 |
+
```python
|
| 27 |
+
import pyaging as pya
|
| 28 |
+
|
| 29 |
+
pya.pred.predict_age(adata, ["stemtoc"])
|
| 30 |
+
```
|
| 31 |
+
|
| 32 |
+
Browse every clock in the [pyaging Clock Catalogue](https://pyaging.readthedocs.io).
|
| 33 |
+
|
| 34 |
+
## Citation
|
| 35 |
+
|
| 36 |
+
Zhu, Tianlei, et al. "An improved epigenetic counter to track mitotic age in cells." Nature Communications 15 (2024): 4211.
|
| 37 |
+
|
| 38 |
+
https://doi.org/10.1038/s41467-024-48649-8
|
config.json
ADDED
|
@@ -0,0 +1,40 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"approved_by_author": "\u2705",
|
| 3 |
+
"citation": "Zhu, Tianlei, et al. \"An improved epigenetic counter to track mitotic age in cells.\" Nature Communications 15 (2024): 4211.",
|
| 4 |
+
"citations": 24,
|
| 5 |
+
"citations_date": "2026-07-05",
|
| 6 |
+
"clock_name": "stemtoc",
|
| 7 |
+
"data_type": "DNA methylation",
|
| 8 |
+
"doi": "https://doi.org/10.1038/s41467-024-48649-8",
|
| 9 |
+
"journal": "Nature Communications",
|
| 10 |
+
"last_author": "Andrew E. Teschendorff",
|
| 11 |
+
"model_type": "95th-percentile methylation aggregation",
|
| 12 |
+
"n_features": 371,
|
| 13 |
+
"notes": "Relative mitotic-age counter based on the 95th percentile across 371 in-vivo-filtered mitotic CpGs.",
|
| 14 |
+
"platform": [
|
| 15 |
+
"Illumina 450K",
|
| 16 |
+
"Illumina EPIC"
|
| 17 |
+
],
|
| 18 |
+
"population": "all ages",
|
| 19 |
+
"predicts": [
|
| 20 |
+
"mitotic age"
|
| 21 |
+
],
|
| 22 |
+
"preprocess": "0.95 quantile",
|
| 23 |
+
"reference_values": true,
|
| 24 |
+
"research_only": null,
|
| 25 |
+
"species": "Homo sapiens",
|
| 26 |
+
"tissue": [
|
| 27 |
+
"multi-tissue",
|
| 28 |
+
"cultured human cells",
|
| 29 |
+
"whole blood"
|
| 30 |
+
],
|
| 31 |
+
"training_target": [
|
| 32 |
+
"population doublings",
|
| 33 |
+
"chronological age"
|
| 34 |
+
],
|
| 35 |
+
"unit": [
|
| 36 |
+
"beta value"
|
| 37 |
+
],
|
| 38 |
+
"version": "v0.3.0",
|
| 39 |
+
"year": 2024
|
| 40 |
+
}
|
stemtoc.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:5f987eb78868b01f463c1576b317fcd7e3c6afc947eb6a96337128865569ac2d
|
| 3 |
+
size 13797
|