Overview
bulk-rnaseq is an open-source data skill for Claude Code and compatible agents, published by K-Dense-AI. Its author describes it as: “End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a gene-level counts matrix, then…”. The project has 46k stars on GitHub and is available under the MIT license. Add it to your setup with `git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/bulk-rnaseq`.
What bulk-rnaseq does
This skill orchestrates a complete, **defensible** bulk RNA-seq differential-expression study, from raw sequencing reads to enriched pathways and figures. It is a router, not a reimplementation: most stages already have dedicated skills in this repo, and this skill connects them in the right order, fills the one real gap (raw reads → a gene-level counts matrix), and enforces the design and QC decisions that determine whether the final result is trustworthy.
Best for
What’s inside
The SKILL.md for bulk-rnaseq is organised into these sections:
- Overview
- When to Use This Skill
- The Pipeline at a Glance
- Two Upstream Paths — Pick One
- Setup
- Quick Start
- Path A — nf-core/rnaseq (recommended)
- Path B — standalone STAR/Salmon (abbreviated)
- Counts → DE → enrichment (both paths)
- Stage-by-Stage Workflow
- The counts → DE bridge (the key glue)
- Common Pitfalls
Installation
Add bulk-rnaseq to your agent with:
git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/bulk-rnaseqReview a skill’s source before installing it — skills can instruct your agent to run commands. This command comes from the skill’s public repository, which is the source of truth for setup steps. New to skills? Read how to install Claude Code skills.
Supported agents
Neither the skill nor its repository names a specific agent. It uses the SKILL.md format, which several agents can load — check the repository for any agent-specific requirements.
License
bulk-rnaseq is published under the MIT license.
Strengths
- Clear MIT license — safe to read and adapt within its terms
- Ships in K-Dense-AI/scientific-agent-skills, an established project with 45,887 GitHub stars
- Actively maintained — repository updated in the last 30 days
- Its repository gained 12,066 GitHub stars over the last 34 days
Author
Topics
Frequently asked questions
- What does bulk-rnaseq do?
- End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a gene-level counts matrix, then hands off to differential expression (pydeseq2), pathway/GSEA enrichment (pathway-enrichment), and publication figures (scientific-visualization). Use whenever the user has bulk RNA-seq reads or quant output and wants a complete, reproducible differential-expression workflow — e.g. "analyze my RNA-seq", "FASTQ to DESeq2", "run nf-core/rnaseq", "STAR/Salmon quantification", "build a counts matrix for DESeq2", or "go from reads to differentially expressed genes and enriched pathways". Routes between an nf-core/rnaseq (Nextflow) path and a standalone STAR/Salmon path, and covers experimental design, strandedness, and QC gates. For single-cell RNA-seq use the scanpy skill instead.
- How do I install bulk-rnaseq?
- Run git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/bulk-rnaseq in your agent, then reload your skills. Review the source at https://github.com/K-Dense-AI/scientific-agent-skills before installing.
- Is bulk-rnaseq free to use?
- Yes. bulk-rnaseq is free and open source under the MIT license, so you can read, run, and adapt it within that license's terms.
- Where does bulk-rnaseq come from?
- bulk-rnaseq ships inside K-Dense-AI/scientific-agent-skills, a repository that contains 42 catalogued skills in total. The repository's 45,887 GitHub stars apply to that whole collection, not to this skill on its own.