bulk-rnaseq
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.
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Install this skill
Run this command in your terminal. No account required — it auto-detects your AI tool and installs the skill file.
npx @skills-hub-ai/cli install scientific-skills-bulk-rnaseqSetup by platform
Install
One-click setup for your editorRun in your project root
npx @skills-hub-ai/cli install scientific-skills-bulk-rnaseq --target claude-codeInstructions
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Frequently asked questions about bulk-rnaseq
What does the bulk-rnaseq skill 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. It's a reusable SKILL.md instruction set that loads into your AI coding assistant on demand, no prompt engineering, no copy-pasting every session.
How do I install the bulk-rnaseq skill?
Run `npx @skills-hub-ai/cli install scientific-skills-bulk-rnaseq` from your terminal. The CLI writes the SKILL.md to the correct location for your AI tool (e.g. ~/.claude/skills/scientific-skills-bulk-rnaseq/ for Claude Code or ~/.cursor/skills/ for Cursor with --target cursor) and adds it to your project's .skills.json lockfile.
Which AI tools does bulk-rnaseq work with?
bulk-rnaseq runs in Claude Code. It follows the open Agent Skills standard (SKILL.md), so the same skill works in every supported tool without modification.
Is the bulk-rnaseq skill free?
Yes. Every skill on skills-hub.ai is free and open-source. There are no premium tiers, paywalls, or usage limits. You only pay for whatever AI assistant you're already using.
How do I use bulk-rnaseq after installing it?
In Claude Code, type `/scientific-skills-bulk-rnaseq` (or whatever slash command the skill registers) and the AI follows the skill's instructions immediately. You can also reference it by name in natural language, your AI loads the skill into context when relevant.
Can I share the bulk-rnaseq skill with my team?
Yes. Commit your project's .skills.json lockfile and teammates run `npx @skills-hub-ai/cli install` (no args) to install every skill at the exact version you pinned. Organization-scoped installs work via skills-hub.ai organizations.