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bio-methylation-array-qc-filtering

100 / 100 · Low risk

Fine to try.

By lilinji/GeneTind-Life-Skills (GitHub) · design · 17 stars · scanned at commit 908229c

Performs probe filtering and sample-level QC on Illumina Infinium methylation arrays (450K / EPIC / EPICv2) to decide which probes and samples to trust. Drops detection-p-failed and low-bead-count probes, removes cross-reactive/non-specific probes (Chen 2013 / Pidsley 2016 lists via maxprobes), excludes SNP-overlapping probes with dropLociWithSnps, and handles sex-chromosome probes. Collapses EPICv2 replicate probes with betasCollapseToPfx and harmonizes across array versions (EPICv2 hg38 vs 45…

Works with any agent that supports SKILL.md skills.

What this skill can do

We found nothing in the files we read that matches our rules. That does not prove the skill is safe: see the limits of static scanning.

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'bio-methylation-array-qc-filtering' ] || [ -L ~/.agents/skills/'bio-methylation-array-qc-filtering' ]; then echo 'A skill folder named bio-methylation-array-qc-filtering already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-methylation-array-qc-filtering' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-methylation-array-qc-filtering' ~/.agents/skills/'bio-methylation-array-qc-filtering' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'bio-methylation-array-qc-filtering' ~/.claude/skills/'bio-methylation-array-qc-filtering' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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