skills.rest
openai
openaiOFFICIAL
Explore all skills by this author →
WebsiteGitHub

ngs-bulk-rnaseq

Routes bulk RNA-seq requests to count-generation QC or differential-expression workflows.

5.3k|765|Updated Mar 4, 2026
Search Tags:#bioinformatics#differential expression#nf-core#rna-seq#ngs#salmon#deSeq2
One-click install
npx skills add https://github.com/openai/plugins --skill ngs-bulk-rnaseq
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ngs-bulk-rnaseq
Source: https://github.com/openai/plugins/tree/main/plugins/ngs-analysis/skills/ngs-bulk-rnaseq
Command: npx skills add https://github.com/openai/plugins --skill ngs-bulk-rnaseq

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Bulk RNA-seq analysis spans two distinct phases—FASTQ-to-count processing and count-matrix differential expression—and choosing the wrong tools, references, or design parameters wastes compute and invalidates results. This Skill acts as a dispatcher that inspects your inputs and routes each request to the correct workflow.

Core Features & Use Cases

  • Workflow Dispatch: Routes FASTQ/BAM inputs to count-generation and QC (nf-core/rnaseq, STAR, Salmon, featureCounts, MultiQC) and count matrices to differential-expression analysis (DESeq2, edgeR, limma).
  • Preflight Validation: Checks tool availability and emits install plans for nf-core, local Snakemake/Salmon, and R/Bioconductor environments before execution.
  • Local Execution Runners: Provides plugin-owned Python runners that produce a standard run envelope with manifests, logs, validation output, and summaries when Docker or Nextflow is unavailable.
  • Use Case: A researcher has paired-end FASTQ files and a sample sheet for a human GRCh38 experiment. The Skill confirms strandedness and genome build, runs a preflight check, launches nf-core/rnaseq for counts and QC, then hands the raw count matrix to differential-expression planning once replicates, design formula, and contrasts are confirmed.

Quick Start

Ask the assistant to inspect your bulk RNA-seq inputs, decide between count generation and differential expression, and prepare a preflight-first run plan.

Frequently Asked Questions about ngs-bulk-rnaseq

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I run a bulk RNA-seq analysis from FASTQ files?▼

Confirm the organism, genome build, read type, and strandedness, then run nf-core/rnaseq with a samplesheet and a genome key such as GRCh38. The pipeline produces raw counts, transcript estimates, and MultiQC summaries for downstream analysis.

What is the difference between count generation and differential expression in RNA-seq?▼

Count generation converts FASTQ or BAM files into raw count matrices using aligners and quantifiers like STAR, Salmon, and featureCounts. Differential expression takes that count matrix plus sample metadata and applies DESeq2, edgeR, or limma with a design formula and contrasts.

nf-core/rnaseq vs local Salmon workflow for RNA-seq quantification?▼

nf-core/rnaseq is preferred when Docker or an HPC runtime is available because it standardizes alignment, quantification, and QC. The local Snakemake/Salmon path suits environments without Docker, registry access, or Nextflow container support.

Can I run RNA-seq analysis without Docker or Nextflow?▼

Yes, the local_light profile runs a compact Snakemake/Salmon workflow through plugin-owned Python runners. These create a standard run envelope with manifests, validation output, logs, and summaries without container dependencies.

When should I not start differential expression analysis?▼

Do not start DESeq2, edgeR, or limma analysis until biological replicates, the design formula, and contrasts are confirmed. Running differential expression on unvalidated metadata or without replicates produces unreliable results.

Related Skills

Explore More Education & Research Skills→
m0atm0at
1

ena-database

Retrieve ENA sequences, reads, and assemblies via REST APIs and FTP.

Community
Advanced
TianGzlabTianGzlab
155

bulkrna-enrichment

Performs pathway enrichment analysis on bulk RNA-seq differential expression results using ORA or GSEA methods.

Official
Intermediate
MubasherMohammedMubasherMohammed

multiqc-reporter

Aggregate bioinformatics QC reports into MultiQC HTML and ClawBio markdown summaries.

Community
Intermediate
awslabsawslabs
13

cell-type-annotation

Assign cell type labels to single-cell RNA-seq clusters using automated classifiers.

Official
Advanced