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Bulk Rnaseq

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 54,643 GitHub stars across a repository of 7 listed skills.

github.com/K-Dense-AI/scientific-agent-skills/skills/bulk-rnaseq (opens in a new tab)

Data as of from the GitHub API; description from the skill's SKILL.md. Report an error

View on GitHub (opens in a new tab)

Add this skill

Claude

Claude Code loads skills from ~/.claude/skills/ (all projects) or .claude/skills/ (one project):

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 bulk-rnaseq folder and upload it under Customize > Skills > + > Upload a skill (code execution must be on).

ChatGPT / Codex

Codex reads skills from .agents/skills/ in a repo or ~/.agents/skills/ for every project:

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

Standalone skills also load in the ChatGPT desktop app.

Cursor

Cursor loads skills from .cursor/skills/ (or ~/.cursor/skills/) and also reads .claude/skills/:

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

Source (checked Oct 7, 2026): code.claude.com/docs/en/skills (opens in a new tab), support.claude.com/en/articles/12512180-using-skills-in-claude (opens in a new tab), learn.chatgpt.com/docs/build-skills (opens in a new tab), cursor.com/docs/context/skills (opens in a new tab)

What this skill does

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.

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.

More skills in K-Dense-AI/scientific-agent-skills

7 skills are listed from this repository.

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FAQ

Bulk Rnaseq FAQ

Still curious? Email info@appsgit.com.

How do I install the Bulk Rnaseq skill?

Copy the bulk-rnaseq folder (the one containing SKILL.md) into ~/.claude/skills/ for Claude Code, .agents/skills/ for Codex or .cursor/skills/ for Cursor. The agent picks it up automatically when a task matches its description.

Is the Bulk Rnaseq skill free?

Yes. The repository is open source under the MIT license.

Is Bulk Rnaseq maintained?

The repository's most recent commit was on Oct 19, 2026. Its latest release is v2.72.0. appsgit only lists skills from repositories with a commit in the last six months.