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bio-workflows-clip-pipeline

End-to-end CLIP-seq pipeline from FASTQ to ENCODE-compliant binding sites, single-nucleotide crosslink maps, annotation, motifs, and (optionally) differential…

Skill by BioTender-max

IndexedNOASSERTION★ 206
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Install

Works with Claude Code, Claude apps, Codex, Cursor, Gemini CLI, GitHub Copilot, VS Code, OpenCode, Goose, Windsurf. Read the repository before you give any tool access to your data.

npx agentmarket install skill/biotender-max-bio-workflows-clip-pipeline

Asks which of your tools to add it to (Claude Code, Codex, Cursor, VS Code, Windsurf, Gemini CLI, Claude Desktop) and shows the change first. See https://agentmart.dev/cli.

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About

End-to-end CLIP-seq pipeline from FASTQ to ENCODE-compliant binding sites, single-nucleotide crosslink maps, annotation, motifs, and (optionally) differential binding. Use when running the full Yeo lab eCLIP / iCLIP / iCLIP2 / iCLIP3 / irCLIP / PAR-CLIP analysis with SMInput control, protocol-specific UMI extraction, ENCODE STAR parameters, CLIPper or Skipper peak calling with stringent log2 FC and -log10 p thresholds, IDR rescue and self-consistency QC, and downstream motif registration with mCross or PEKA.

Use cases: data

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Permissions

What this skill can do and what it asks for, from its SKILL.md. Checked Oct 25, 2026.

Tools
No tools found
Secrets
None asked for
Install scripts
None found
Runs as
Shell scripts

Network hosts it talks to 1

  • codeload.github.com · found in install command

Files it touches

  • ~/.claude/skills/bio-workflows-clip-pipeline

What's inside

Skill name
bio-workflows-clip-pipeline
Description
End-to-end CLIP-seq pipeline from FASTQ to ENCODE-compliant binding sites, single-nucleotide crosslink maps, annotation, motifs, and (optionally) differential binding. Use when running the full Yeo lab eCLIP / iCLIP / iCLIP2 / iCLIP3 / irCLIP / PAR-CLIP analysis with SMInput control, protocol-specific UMI extraction, ENCODE STAR parameters, CLIPper or Skipper peak calling with stringent log2 FC and -log10 p thresholds, IDR rescue and self-consistency QC, and downstream motif registration with mCross or PEKA.
License
NOASSERTION
Instructions
323 lines in SKILL.md · view on GitHub

Before installing

  • Ships executable scripts

Agent Skills spec issues

  • name: "bio-workflows-clip-pipeline" does not match folder "clip-pipeline"

Files (3)

  • SKILL.md
  • clip_full_pipeline.sh · examples/
  • usage-guide.md

The license isn't open source, so the instructions aren't shown here. Read SKILL.md on GitHub

More from BioTender-max/awesome-bio-agent-skills

Signals

Stars
206
Forks
36
Open issues
1
Last commit (this folder)
May 25, 2026 (5 months ago)
Last release
Jul 1, 2026 (4 months ago)

From GitHub (fetched Oct 24, 2026).

Details

License
NOASSERTION
Repository
github.com/BioTender-max/awesome-bio-agent-skills
Website
biotender-max.github.io/awesome-bio-agent-skills/
First seen
Oct 24, 2026
Last checked
Oct 24, 2026
Source
GitHubgithub-graphql

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bio-workflows-clip-pipeline skill. Agent Mart. https://agentmart.dev/skills/biotender-max-bio-workflows-clip-pipeline (last updated 2026-10-24)