Methylation Clock

What it does

When your agent uses it

• Research & Science work in your project

Example prompts

• “/methylation-clock”

Requirements

• Python 3

Workflow steps

4 steps, taken from the first numbered list in SKILL.md.

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

What it can do on your machine

Read from SKILL.md and the folder at commit 5e045e3. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Ships script files (Python), which the agent can run.

  Shell commands in SKILL.md call:

  • python
  • pip

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Methylation Clock loads about 922 tokens when it runs. Until then it costs about 31 tokens; SKILL.md has 246 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~31

When it runs · the whole SKILL.md, loaded when a task matches

~922

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from ClawBio/ClawBio at commit 5e045e3, republished under its MIT licence (© ClawBio). 246 words, ~922 tokens.

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

metadata.tags

epigenetics, methylation, aging, clock, pyaging, GEO, illlumina-450k, EPIC

pip install pyaging>=0.1

# 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

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

© ClawBio, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 5 other files in skills/methylation-clock of ClawBio/ClawBio.

• SKILL.md
• data/GSE139307_small.csv.gz
• data/PROVENANCE.md
• methylation_clock.py
• tests/test_methylation_clock.py
• tests/test_sha256_delegation.py

Open the folder on GitHubat commit 5e045e3

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.

• BioTender-max/awesome-bio-agent-skillsskills/clawbio/methylation-clock