Pipeline Chipseq

Q: What is a Claude Code skill and how does the Pipeline Chipseq skill fit in?

A Claude Code skill is a SKILL.md file that lives under ~/.claude/skills/<name>/ and tells the Claude Code CLI agent how to perform a specific task (instructions, prompts, allowed tools). Skills are auto-discovered at session start. Pipeline Chipseq is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Engineering category. Learn more at https://claudskills.com/learn/what-is-skill-md/.

Category: Engineering · Sub-category: devops · Last updated: 2026-08-02

tool:docker

Execute ENCODE ChIP-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides stage-by-stage Nextflow execution with Docker containers and cloud deployment. Use when users need to process ChIP-seq data following ENCODE standards, run peak calling with MACS2, perform IDR analysis, or generate signal tracks. Trigger on: ChIP-seq pipeline, run ChIP-seq, process ChIP-seq, MACS2 peak calling, IDR analysis, ChIP-seq FASTQ processing.

Security AStatic scan found no risk patternsHow grading works ›

What this skill does

Pipeline Chipseq is a community-contributed Claude Code skill in the devops sub-category. It ships as a SKILL.md file that Claude Code auto-discovers under ~/.claude/skills/pipeline-chipseq/ and loads when your prompt matches the skill's trigger.

When to invoke it: Use when users need to process ChIP-seq data following ENCODE standards, run peak calling with MACS2, perform IDR analysis, or generate signal tracks. Trigger on: ChIP-seq pipeline, run ChIP-seq, process ChIP-seq, MACS2 peak calling, IDR analysis, ChIP-seq FASTQ processing.

Who uses this skill

The Pipeline Chipseq Claude Code skill is built for software engineers, backend developers, full-stack teams, and technical leads building and maintaining production systems. It's part of ClaudSkills (also referred to as Claude Skills or Claude Code Skills) — the open community-curated registry of 174,000+ SKILL.md files for Anthropic's Claude Code agent and the wider Claude ecosystem (Claude API, Claude Agent SDK).

How to install

Free

Manual install (2 steps)

mkdir -p ~/.claude/skills/pipeline-chipseq
curl -L https://claudskills.com/skills/pipeline-chipseq/SKILL.md \
  -o ~/.claude/skills/pipeline-chipseq/SKILL.md

Or just download SKILL.md directly and drop it into ~/.claude/skills/pipeline-chipseq/. Claude Code auto-discovers it on next session.

Skills live at ~/.claude/skills/pipeline-chipseq/SKILL.md on macOS/Linux, or %USERPROFILE%\.claude\skills\pipeline-chipseq\SKILL.md on Windows. See the full install guide for step-by-step instructions.

📱 Install from your phone or desktop Telegram

Open @claudskills_bot on Telegram, tap Open Desktop App, and the desktop app installs this skill for you. Or share the bot link with a colleague — they get the same one-tap install. Learn more →

Pro

One-click install via the desktop app

The ClaudSkills desktop app installs any skill directly into ~/.claude/skills/ with one click — no terminal required. Pro starts at $9/mo or $149 lifetime.

Pro

For the full experience including quality scoring and one-click install features for each skill — upgrade to Pro.

See pricing → Download desktop app

Frequently asked questions

How do I install the Pipeline Chipseq Claude Code skill?

Install via the ClaudSkills desktop app (one click) or copy SKILL.md from the source repository to ~/.claude/skills/pipeline-chipseq/SKILL.md and restart Claude Code. Both flows are detailed at claudskills.com/install/.

What does the Pipeline Chipseq skill do?

Is this skill free to install?

Yes. ClaudSkills is an open registry — every skill keeps its source repository's license, and manual install via copy is free. ClaudSkills Pro ($9/mo, $79/yr, or $149 one-time) adds one-click install via the desktop app and a multi-signal Quality Score.

When should I use the Pipeline Chipseq skill?

Use Pipeline Chipseq when your Claude Code task falls under the Engineering category — specifically in the devops area. Claude Code auto-discovers installed skills and invokes the right one based on the task description, so you can also ask Claude directly (e.g. "use Pipeline Chipseq" or describe the task and let Claude pick). Browse related skills at /category/engineering/.

What is a Claude Code skill and how does the Pipeline Chipseq skill fit in?

A Claude Code skill is a SKILL.md file that lives under ~/.claude/skills/<name>/ and tells the Claude Code CLI agent how to perform a specific task (instructions, prompts, allowed tools). Skills are auto-discovered at session start. Pipeline Chipseq is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Engineering category. Learn more at /learn/what-is-a-claude-skill/.

Attribution & license

Source: https://github.com/majiayu000/claude-skill-registry/blob/HEAD/skills/ai-ml/pipeline-chipseq/SKILL.md
License: MIT
Author: majiayu000
Website: https://majiayu000.github.io/claude-skill-registry/

Cite this skill

If you reference this skill in a blog post, paper, or documentation, you can cite it as:

APA

majiayu000. (2026). Pipeline Chipseq [Claude Code skill]. ClaudSkills. https://claudskills.com/skills/pipeline-chipseq/

BibTeX

@misc{pipeline-chipseq-2026,
  author    = {majiayu000},
  title     = {Pipeline Chipseq [Claude Code skill]},
  year      = {2026},
  publisher = {ClaudSkills},
  url       = {https://claudskills.com/skills/pipeline-chipseq/}
}

Embed this skill

Promote, attribute, or link this skill from your own README, blog post, or documentation. All three snippets are free to use — no sign-up, no API key. More distribution surfaces →

Badge

[![ClaudSkills](https://claudskills.com/badge/pipeline-chipseq.svg)](https://claudskills.com/skills/pipeline-chipseq/?utm_source=badge&utm_medium=readme&utm_campaign=skill_badge)

Security scan

Grade A · scanned 2026-08-02 — free static scan against the OWASP Agentic Skills Top 10.

The scan flagged 1 of 10 categories (network), including lower-severity patterns. Patterns shown inside code fences are weighted as examples rather than instructions — read the grading methodology for what this does and does not guarantee.

✓ Prompt injection
✓ Data exfiltration
✓ Supply chain
✓ Reverse shell
✓ Credentials
✓ Execution
✓ Filesystem
✓ Persistence
✓ Obfuscation
⚠ Network

Show this grade on your repo (click to copy):

[![Security: A](https://img.shields.io/badge/Security-A-2e7d32)](https://claudskills.com/skills/pipeline-chipseq/#security)

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Browse all Engineering skills in the ClaudSkills registry, or explore these other picks from the same category:

Browse all Engineering skills → Top 100 skills

Part of ClaudSkills — the open registry for Claude Skills & Claude Code Skills. · What's New · Install guide · About · llms.txt

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