Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add inflexa-ai/inflexa --skill dna-methylationgit clone --depth 1 https://github.com/inflexa-ai/inflexaWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/inflexa-ai/inflexa/dna-methylation)<a href="https://agentmods.dev/skills/inflexa-ai/inflexa/dna-methylation"><img src="https://agentmods.dev/badge/skills/inflexa-ai/inflexa/dna-methylation/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/inflexa-ai/inflexa/dna-methylation"><img src="https://agentmods.dev/badge/skills/inflexa-ai/inflexa/dna-methylation.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00040 | $0.02682 |
| Opus 5 | $0.00020 | $0.01341 |
| Sonnet 5 | $0.00008 | $0.00536 |
| Haiku 4.5 | $0.00004 | $0.00268 |
Grade A, and why
dna-methylation scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured yesterday.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 181 lines — stays where its author put it; the contents beside it link to each section on GitHub.
DNA Methylation Analysis
Comprehensive guidelines for methylation array processing, bisulfite sequencing analysis, differential methylation, epigenetic clocks, cell type deconvolution, and epigenome-wide association studies.
Environment Constraint: Array Annotation Is Not Staged
Read this before planning any array pipeline. The analysis packages (minfi, ChAMP, DMRcate, missMethyl, EpiDISH, methylclock) are installed, but the Illumina array manifest and annotation packages they depend on are not — no IlluminaHumanMethylation450kanno.*, IlluminaHumanMethylationEPICanno.*, IlluminaHumanMethylationEPICv2anno.*, and no matching *manifest package. There is also no network egress, so they cannot be installed at runtime, and Bioconductor's ExperimentHub/AnnotationHub fetches fail even though those client packages are present.
What this means in practice:
| Step | Status |
|---|---|
IDAT → RGChannelSet → normalized betas (minfi, ChAMP) |
Cannot run. Requires the manifest package to decode probe addresses. |
Genomic mapping / probe annotation (mapToGenome(), getAnnotation()) |
Cannot run. Requires the anno package. |
Array DMR calling (DMRcate::cpg.annotate(datatype = "array")) |
Cannot run. Resolves probe coordinates from the anno package. |
Deconvolution from an existing beta matrix (EpiDISH) |
Runs. Self-contained references, no annotation dependency. |
Epigenetic clocks (methylclock) |
Runs on a beta matrix, but needs clock coefficients — see references/methylclock-api.md. |
Bisulfite-seq (dmrseq / DSS) |
Downstream only. Both run on a methylation/coverage matrix you already have; bisulfite read alignment and methylation extraction are upstream of this pack (see §2). |
How to proceed: verify the annotation package actually loads before building a pipeline around it. If it does not, say so plainly — name the missing package and the step it blocks — and then do the analysis the data does support. A beta or M-value matrix that arrives already processed (from GEO, a collaborator, or an upstream step) still supports DMP testing, deconvolution, clocks, and EWAS modelling; only the probe-to-genome annotation is missing, and results can be reported by CpG ID. Do not silently substitute a different array's annotation, and do not present an unannotated result as though it were annotated.
What ships with it
5 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- yesterday First seen · 181 lines · 40 tokens per session scan A cf21ba020c9f
dna-methylation is a skill published in the GitHub repository inflexa-ai/inflexa (33 stars, last pushed today), licensed Apache-2.0. It adds 40 tokens to every session and 2,682 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-09.
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