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bedpe-format-handling

100 / 100 · Low risk

Fine to try.

By HolobiomicsLab/asb-skill-collections (GitHub) · coding · 16 stars · scanned at commit bf028f4

Use when your ChIP-Seq input is paired-end sequencing data stored in BEDPE format (e.g., CTCF_PE_ChIP_chr22_50k.bedpe.gz), and you need to estimate fragment length and call peaks while respecting the paired nature of the reads rather than treating them as independent single-end alignments.

Works with any agent that supports SKILL.md skills.

This skill is no longer available at its GitHub address. The information below is from the last time we could read it and may be out of date.

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/'bedpe-format-handling' ] || [ -L ~/.agents/skills/'bedpe-format-handling' ]; then echo 'A skill folder named bedpe-format-handling already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/HolobiomicsLab/asb-skill-collections' "$d" && git -C "$d" checkout --quiet 'bf028f481d363bb69a4047acecffccb62ea40705' -- 'collections/epigenomics/v1/skills/bedpe-format-handling' && mkdir -p ~/.agents/skills && cp -R "$d"/'collections/epigenomics/v1/skills/bedpe-format-handling' ~/.agents/skills/'bedpe-format-handling' && 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/'bedpe-format-handling' ~/.claude/skills/'bedpe-format-handling' (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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