bio-methylation-array-preprocessing

bio-methylation-array-preprocessing is a skill for Claude Code, Codex from FridrichMethod/awesome-skills. It costs 251 tokens per session (4,706 once invoked), scanned A, original, no licence file.

A preprocessing workflow that converts raw Illumina methylation-array IDAT files into beta or M values for analysis. It covers the 450K, EPIC, and EPICv2 arrays and supports sesame or minfi processing.

In plain words
What is it for?
Use it to read IDAT files, process array signals, convert them into beta or M matrices, and create genomic methylation data objects.
Why use it?
It handles the different probe chemistries used by these arrays and explains why raw measurements can be distorted. This produces a more suitable representation for downstream analysis.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

Install

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.

agentmods
npx agentmods add skills/fridrichmethod/awesome-skills/array-preprocessing
Any agent
npx skills add FridrichMethod/awesome-skills --skill array-preprocessing
Clone the repo
git clone --depth 1 https://github.com/FridrichMethod/awesome-skills

Made for: Claude Code, Codex.

Wrote 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.

agentmods badge for bio-methylation-array-preprocessing

README.md
[![agentmods](https://agentmods.dev/badge/skills/fridrichmethod/awesome-skills/array-preprocessing.svg)](https://agentmods.dev/skills/fridrichmethod/awesome-skills/array-preprocessing)
Your own site
<a href="https://agentmods.dev/skills/fridrichmethod/awesome-skills/array-preprocessing"><img src="https://agentmods.dev/badge/skills/fridrichmethod/awesome-skills/array-preprocessing.svg" alt="Measured on agentmods" height="20"></a>
Per session 251 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 4,706 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
Origin unknown No closer match found in the catalogue.
Token cost

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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00251 $0.04706
Opus 5 $0.00125 $0.02353
Sonnet 5 $0.00050 $0.00941
Haiku 4.5 $0.00025 $0.00471

Measured 2d ago against content hash b21c17d47139, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-06, from the pricing page.

Security

Grade A, and why

bio-methylation-array-preprocessing 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 2d ago.

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.

skills/array-preprocessing/SKILL.md · 187 lines

The source is not reproduced here

A licence we could not identify

The repository carries a LICENSE file, but it is custom or dual enough that GitHub cannot name it and neither can this catalogue. Unknown terms are not permission, so the body is not copied here. Read the licence at the source and decide for yourself.

Read it on GitHub

Files

What ships with it

2 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.

Changes

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.

  1. 2d ago First seen · 187 lines · 251 tokens per session scan A b21c17d47139

Subscribe to this mod's changes

bio-methylation-array-preprocessing is a skill published in the GitHub repository FridrichMethod/awesome-skills (14 stars, last pushed 6d ago), with no licence file. It adds 251 tokens to every session and 4,706 once invoked, about $0.0013 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 2026-09-03.

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