Description
bulk-rnaseq is an agent skill that prepares bulk RNA-seq reads and quantification output for a reproducible gene-level comparison. It takes FASTQ files, along with Salmon, STAR or featureCounts output, and gets them ready for differential expression. It owns sample validation, the recipes that turn reads into counts, and the handoff of counts and metadata to later steps. Statistical fitting and enrichment analysis are left to specialist skills. The skill defines defensible work as three things: reproducible, with pinned tool versions, containers where possible, recorded parameters and fixed random seeds; quality-gated, with QC inspected and acted on before, during and after quantification; and statistically sound, with adequate replication, a design that matches the biology, correct handling of counts, and FDR-controlled testing. The pipeline it describes runs FastQC and trimming, then alignment and quantification with STAR or Salmon, then counts, then differential expression with pydeseq2, then enrichment, then figures. It covers nf-core/rnaseq as well as standalone quantification. Use it when you are setting up a bulk RNA-seq comparison.…
Highlights
- Sample validation and reads-to-counts recipes
- Works with Salmon, STAR and featureCounts output
- Covers nf-core/rnaseq and standalone quantification
- Quality checks at each stage
- Hands counts and metadata to downstream skills
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bulk-rnaseq FAQ
What does the skill prepare?
Bulk RNA-seq reads and quantification output, ready for gene-level differential expression.
Which tools does it use?
FastQC and trimming, STAR or Salmon for alignment and quantification, pydeseq2 for differential expression, and featureCounts output as an input.
What does 'defensible' mean here?
The skill defines it as reproducible, quality-gated and statistically sound, with pinned versions, QC at each stage, and FDR-controlled testing.
Does it do the statistics?
Not all of it. Statistical fitting and enrichment are left to specialist skills.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill bulk-rnaseq.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best bulk-rnaseq alternatives?
Popular alternatives to bulk-rnaseq include pydeseq2, gget and biopython. See all bulk-rnaseq alternatives