deepTools (Claude Skill)

NGS analysis toolkit.

Type	Claude Skill
Supplier	K-Dense Inc. (community OSS)
Availability	GA — part of the actively maintained K-Dense scientific-agent-skills collection
Pricing	Free / OSS (BSD)
Capabilities	Read/Write — Claude runs the skill’s Python locally (Bash), not as an MCP tool

How to install

• Also packaged in the SciAgent-Skills collection (jaechang-hits (community OSS, CC BY 4.0)): clone jaechang-hits/SciAgent-Skills and run /plugin install sciagent-skills in Claude Code (or copy skills/genomics-bioinformatics/interval-ops/deeptools-ngs-analysis into ~/.claude/skills/).
• Claude Code / Claude.ai — Skills CLI (recommended):

  npx skills add K-Dense-AI/scientific-agent-skills
  

  Installs the K-Dense collection; enable the deeptools skill when prompted. Works across Claude Code, Cursor, and Codex via the Agent Skills spec (requires Node ≥ 18).

• Claude Code / Claude Desktop — manual clone:

  git clone https://github.com/K-Dense-AI/scientific-agent-skills
  cp -r scientific-agent-skills/skills/deeptools ~/.claude/skills/
  

  Project-scoped alternative: copy into .claude/skills/ instead of ~/.claude/skills/. The skill declares its own Python dependencies in its SKILL.md; install them (the K-Dense skills generally use uv / pip) when prompted on first use.

What it does

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

Primary use cases: NGS analysis toolkit.

Notes

Distributed as a SKILL.md (plus code examples) in the K-Dense collection — Claude executes it locally via Bash/Python rather than as an MCP server. Upstream license: BSD. The skill name to enable after install is deeptools.

Sources

• K-Dense-AI/scientific-agent-skills
• skills/deeptools/SKILL.md

---

Installed this tool?

Share feedback — install path, OS, errors, workarounds. The form opens with this tool pre-selected and a link back to this page.