---
name: methylation-clock
description: Compute epigenetic age from DNA methylation arrays using PyAging clocks from GEO accessions or local files.
license: MIT
metadata:
  version: 0.1.0
  tags:
  - epigenetics
  - methylation
  - aging
  - clock
  - pyaging
  - GEO
  - illlumina-450k
  - EPIC
  openclaw:
    requires:
      bins:
      - python3
    always: false
    emoji: 🧪
    homepage: https://github.com/ClawBio/ClawBio
    os:
    - darwin
    - linux
    install:
    - kind: pip
      package: pandas
    - kind: pip
      package: numpy
    - kind: pip
      package: matplotlib
    - kind: pip
      package: pyaging
    trigger_keywords:
    - epigenetic age
    - methylation clock
    - pyaging
    - horvath
    - grimage
    - dunedinpace
    - GEO
    - GSE
---

# Methylation Clock

## Domain Decisions

Epigenetic age workflows are difficult to reproduce because preprocessing and clock inputs differ across tools and publications.
This skill standardizes a PyAging-first pipeline from ingestion to report generation, with explicit reproducibility outputs.

### Core Capabilities

1. Accepts exactly one input source: GEO accession (`--geo-id`) or local methylation file (`--input`).
2. Applies notebook-aligned preprocessing (female derivation and EPICv2 aggregation by default).
3. Converts tabular data to AnnData and runs one or more methylation clocks.
4. Exports predictions, missing-feature diagnostics, metadata, figures, and reproducibility artifacts.

### Input Contract

- Exactly one input source:
  - GEO accession with `--geo-id` (example: `GSE139307`)
  - Local file with `--input` (`.pkl`, `.pickle`, `.csv`, `.tsv`, `.csv.gz`, `.tsv.gz`)
- Required output directory via `--output`
- Optional clock list via `--clocks`

### Demo And Usage

Demo fixture provenance and checksum are documented in `skills/methylation-clock/data/PROVENANCE.md`.

Install optional methylation-clock dependency (not part of the global base requirements):

```bash
pip install pyaging>=0.1
```

```bash
# Demo
python skills/methylation-clock/methylation_clock.py \
  --input skills/methylation-clock/data/GSE139307_small.csv.gz \
  --output /tmp/methylation_clock_demo

# GEO input
python skills/methylation-clock/methylation_clock.py \
  --geo-id GSE139307 \
  --output /tmp/methylation_clock_geo

# Local methylation file
python skills/methylation-clock/methylation_clock.py \
  --input my_methylation.pkl \
  --clocks Horvath2013,AltumAge,PCGrimAge,GrimAge2,DunedinPACE \
  --output /tmp/methylation_clock_local
```

### Output Structure

```
methylation_clock_report/
├── report.md
├── figures/
│   ├── clock_distributions.png
│   └── clock_correlation.png
├── tables/
│   ├── predictions.csv
│   ├── prediction_summary.csv
│   ├── missing_features.csv
│   └── clock_metadata.json
└── reproducibility/
    ├── commands.sh
    ├── environment.yml
    └── checksums.sha256
```

## Safety Rules

1. ClawBio is local-first: user methylation data must remain on-device.
2. The skill refuses non-empty output directories to avoid silent overwrite.
3. Reports must include this disclaimer: "ClawBio is a research and educational tool. It is not a medical device and does not provide clinical diagnoses. Consult a healthcare professional before making any medical decisions."

## Agent Boundary

1. Route methylation clock requests to `skills/methylation-clock/methylation_clock.py`.
2. Do not infer clinical diagnosis or treatment from clock estimates.
3. Trigger terms include: epigenetic age, methylation clock, Horvath, GrimAge, DunedinPACE, GEO, GSE.
4. Valid downstream chaining: `rnaseq-de` for transcriptomic-aging contrasts and `equity-scorer` for cohort context.


---
Source attribution: ClawBio
Original project: https://github.com/ClawBio/ClawBio
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Mega AI Hub.

## Upstream license notice

MIT License

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



# Mega AI Hub resource metadata

Creator / publisher: ClawBio
Original project: https://github.com/ClawBio/ClawBio
Attribution basis: Exact package in biomedical source index and publisher source table

Fields of work: Data & Analytics, Education & Research
Roles: Business Intelligence Analyst, Data Scientist, Researcher
Specialties: API
Tools: Matplotlib, Numpy, Pandas, Pyaging
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: ff4fb2a17b6ea6d2554dbfd22f7458b5bbe6b6a5d346dda45d4d38e0c62d4844
Metadata reviewed: 2026-10-27
This metadata supersedes earlier Mega AI Hub catalog attribution. Original instruction and supporting files are preserved.