ngs-bulk-rnaseq-counts-qc Skill
Run or plan bulk RNA-seq FASTQ-to-count processing with sample-sheet, strandedness, genome annotation, alignment or pseudoalignment, MultiQC, and count-matrix QC checks. Published by openai in plugins.
What is ngs-bulk-rnaseq-counts-qc Skill?
Run or plan bulk RNA-seq FASTQ-to-count processing with sample-sheet, strandedness, genome annotation, alignment or pseudoalignment, MultiQC, and count-matrix QC checks. Published by openai in plugins. This profile combines repository metadata with install, compatibility, and usage signals so developers can quickly decide whether it fits their agent workflow before opening the source repository.
Automated repository signals based on public metadata such as recency, license, installation evidence, and adoption. These are not a security audit or endorsement.
Key capabilities
- Includes SKILL.md support
- Reusable instructions support
- Deployment
- Deployment use cases
Technical details
- Install or run with Copy skill directory
When to use ngs-bulk-rnaseq-counts-qc Skill
- Use it for deployment.
Built with
Editorial notes
Source
- Creator: openai
- Repository: openai/plugins
- Skill file: plugins/ngs-analysis/skills/ngs-bulk-rnaseq-counts-qc/SKILL.md
What it does
Run or plan bulk RNA-seq FASTQ-to-count processing with sample-sheet, strandedness, genome annotation, alignment or pseudoalignment, MultiQC, and count-matrix QC checks.
Skill instructions
Bulk RNA-seq Counts QC Use this skill for bulk RNA-seq read processing, quantification, and count-matrix generation. If the user already has a count matrix and wants contrasts or statistics, use ngs-bulk-rnaseq-differential-expression. Essential Inputs Confirm: - FASTQ or aligned-read inputs and paired-end/single-end status - organism, genome build, FASTA, GTF, and gene ID convention - strandedness or permission to infer strandedness - sample sheet with biological condition, replicate, batch, and library metadata - desired quantification: gene counts, transcript estimates, or both - alignment strategy: STAR/Salmon, Salmon-only, featureCounts from BAMs, or existing lab protocol Route Prefer nf-core/rnaseq for standard processing when a stable container or HPC runtime is available. Use the locallight Snakemake/Salmon path for small local/devbox feasibility runs when Docker, registry egress, or Nextflow process containers are the blocker. The plugin-owned local runner is: bash python plug
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Frequently asked questions
What is ngs-bulk-rnaseq-counts-qc?
ngs-bulk-rnaseq-counts-qc is a open-source AI agent skill with Copy skill directory. Run or plan bulk RNA-seq FASTQ-to-count processing with sample-sheet, strandedness, genome annotation, alignment or pseudoalignment, MultiQC, and count-matrix QC checks.
Who is ngs-bulk-rnaseq-counts-qc best for?
ngs-bulk-rnaseq-counts-qc is best for reusing agent instructions, scripts, and references, deployment workflows.
How do I install ngs-bulk-rnaseq-counts-qc?
Install or run ngs-bulk-rnaseq-counts-qc using Copy skill directory. Check ngs-bulk-rnaseq-counts-qc for the latest setup command.
Is ngs-bulk-rnaseq-counts-qc actively maintained?
ngs-bulk-rnaseq-counts-qc may need a closer maintenance check before production use.
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