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ClaudSkills / Science & Research / biology-medicine

Bulk Rnaseq

Category: Science & Research  ·  Sub-category: biology-medicine  ·  Last updated:
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.

About this skill (catalog notes)

Bulk Rnaseq includes a dedicated installation section; 5 code blocks for direct copy-paste. At roughly 1,736 words the SKILL.md is on the longer end of the catalog distribution.

Source
k-dense.ai
License
MIT
Original author
K-Dense-AI
Indexed lastmod
Catalog position
Science & Research · biology-medicine
Indexed related skills
10

How Bulk Rnaseq fits the catalog

Bulk Rnaseq sits in the Science & Research category under the biology-medicine sub-topic in the ClaudSkills catalog. There are 10 related skills indexed alongside it; comparing a few before installing usually reveals which fits your workflow best.

These notes are auto-generated from features detected in the SKILL.md file and from this catalog's structure — they aren't part of the source repository.

What this skill does

Bulk Rnaseq is a community-contributed Claude Code skill in the biology-medicine sub-category. It ships as a SKILL.md file that Claude Code auto-discovers under ~/.claude/skills/bulk-rnaseq/ and loads when your prompt matches the skill's trigger.

When to invoke it: Use whenever the user has bulk RNA-seq reads or quant output and wants a complete, reproducible differential-expression workflow — e.g.

Who uses this skill

The Bulk Rnaseq Claude Code skill is built for researchers, data scientists, academics, and analysts working with complex data and scientific literature. It's part of ClaudSkills (also referred to as Claude Skills or Claude Code Skills) — the open community-curated registry of 93,000+ SKILL.md files for Anthropic's Claude Code agent and the wider Claude ecosystem (Claude API, Claude Agent SDK).

How to install

Free

Manual install (2 steps)

mkdir -p ~/.claude/skills/bulk-rnaseq
curl -L https://claudskills.com/skills/bulk-rnaseq/SKILL.md \
  -o ~/.claude/skills/bulk-rnaseq/SKILL.md

Or just download SKILL.md directly and drop it into ~/.claude/skills/bulk-rnaseq/. Claude Code auto-discovers it on next session.

Skills live at ~/.claude/skills/bulk-rnaseq/SKILL.md on macOS/Linux, or %USERPROFILE%\.claude\skills\bulk-rnaseq\SKILL.md on Windows. See the full install guide for step-by-step instructions.

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Open @claudskills_bot on Telegram, tap Open Desktop App, and the desktop app installs this skill for you. Or share the bot link with a colleague — they get the same one-tap install. Learn more →

Pro

One-click install via the desktop app

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Pro

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See pricing → Download desktop app

Frequently asked questions

How do I install the Bulk Rnaseq Claude Code skill?
Install via the ClaudSkills desktop app (one click) or copy SKILL.md from the source repository to ~/.claude/skills/bulk-rnaseq/SKILL.md and restart Claude Code. Both flows are detailed at claudskills.com/install/.
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.
Is this skill free to install?
Yes. ClaudSkills is an open registry — every skill keeps its source repository's license, and manual install via copy is free. ClaudSkills Pro ($9/mo, $79/yr, or $149 one-time) adds one-click install via the desktop app and a multi-signal Quality Score.
When should I use the Bulk Rnaseq skill?
Use Bulk Rnaseq when your Claude Code task falls under the Science & Research category — specifically in the biology medicine area. Claude Code auto-discovers installed skills and invokes the right one based on the task description, so you can also ask Claude directly (e.g. "use Bulk Rnaseq" or describe the task and let Claude pick). Browse related skills at /category/science/.
What is a Claude Code skill and how does the Bulk Rnaseq skill fit in?
A Claude Code skill is a SKILL.md file that lives under ~/.claude/skills/<name>/ and tells the Claude Code CLI agent how to perform a specific task (instructions, prompts, allowed tools). Skills are auto-discovered at session start. Bulk Rnaseq is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Science & Research category. Learn more at /learn/what-is-a-claude-skill/.

Attribution & license

Cite this skill

If you reference this skill in a blog post, paper, or documentation, you can cite it as:

APA
K-Dense-AI. (2026). Bulk Rnaseq [Claude Code skill]. ClaudSkills. https://claudskills.com/skills/bulk-rnaseq/
BibTeX
@misc{bulk-rnaseq-2026,
  author    = {K-Dense-AI},
  title     = {Bulk Rnaseq [Claude Code skill]},
  year      = {2026},
  publisher = {ClaudSkills},
  url       = {https://claudskills.com/skills/bulk-rnaseq/}
}

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