# Bulk Rnaseq (agent skill)

> Bulk Rnaseq is an agent skill (a SKILL.md file) from K-Dense-AI/scientific-agent-skills. Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression. It works with Claude Code, Codex, Cursor, Gemini CLI and GitHub Copilot and has 47,813 GitHub stars across a repository of 7 listed skills.

Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression. Covers nf-core/rnaseq and standalone quantification, biological replication, strandedness, reference provenance, validated count assembly and a PyDESeq2 handoff. Use for FASTQ-to-counts analysis, nf-core/rnaseq configuration, STAR/Salmon quantification, or building a counts matrix for DESeq2. For single-cell data use scanpy; for statistical fitting alone use pydeseq2.

## Key facts

| Fact | Value |
|---|---|
| Repository | https://github.com/K-Dense-AI/scientific-agent-skills |
| Skill path | skills/bulk-rnaseq/SKILL.md |
| Skill name | bulk-rnaseq |
| GitHub stars | 47,813 |
| Installs on skills.sh | not listed |
| License | MIT |
| Skills in repo | 7 |
| Plugin marketplace | no |
| Official | no |
| Works with | Claude Code, Codex, Cursor, Gemini CLI, GitHub Copilot |
| Category | Data & analysis |
| Last commit | Oct 5, 2026 |

## When it triggers

- Use for FASTQ-to-counts analysis, nf-core/rnaseq configuration, STAR/Salmon quantification, or building a counts matrix for DESeq2.
- use scanpy; for statistical fitting alone use pydeseq2.

## Add this skill

### Claude Code

```sh
git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git
cp -r scientific-agent-skills/skills/bulk-rnaseq ~/.claude/skills/bulk-rnaseq   # personal, or .claude/skills in a project
```

In the Claude apps, zip the skill folder and upload it under Customize > Skills > + > Upload a skill (code execution must be on).

### ChatGPT / Codex

```sh
git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git
cp -r scientific-agent-skills/skills/bulk-rnaseq .agents/skills/bulk-rnaseq   # repo; ~/.agents/skills for all projects
```

### Cursor

```sh
git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git
cp -r scientific-agent-skills/skills/bulk-rnaseq .cursor/skills/bulk-rnaseq   # project; ~/.cursor/skills for all projects
```

Sources (checked 2026-10-07): https://code.claude.com/docs/en/skills, https://support.claude.com/en/articles/12512180-using-skills-in-claude, https://learn.chatgpt.com/docs/build-skills, https://cursor.com/docs/context/skills

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Canonical page: https://appsgit.com/skills/k-dense-ai-bulk-rnaseq
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