methylation-clock
Compute epigenetic age from DNA methylation arrays using PyAging clocks from GEO accessions or local files.
npx skills add BioTender-max/awesome-bio-agent-skills --skill methylation-clock --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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 pyagi
- Domain Decisions
- Core Capabilities
- Input Contract
- Demo And Usage
- Output Structure
- Safety Rules
- Agent Boundary
pip install pyaging>=0.1 Demo python skills/methylation-clock/methylation_clock.py \ GEO input Local methylation file
What does the methylation-clock skill do?
Compute epigenetic age from DNA methylation arrays using PyAging clocks from GEO accessions or local files.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill methylation-clock --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.