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bulk-rnaseq

Category: life-sciences · License: MIT · Version: 1.1 · Includes scripts Tags: RNA-seq, transcriptomics, differential expression, alignment, bioinformatics

When to use it

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.

Example requests

Ask your agent in plain language, for example:
  • “I have 12 paired-end FASTQ files from a mouse liver drug-treatment experiment. Can you take me from reads all the way to differentially expressed genes?”
  • “I ran Salmon on 8 samples (quant.sf files in salmon_out/sample/) against GRCh38 Ensembl release 110. How do I get a counts.csv and metadata file that PyDESeq2 will accept? PyDESeq2 errors out saying my counts aren’t integers.”*
  • “My collaborator sequenced treated vs. untreated tumor organoids in triplicate, but the treated ones were all run on a different lane and day than the controls. I want to know which pathways are changing between the two groups. How should I proceed?”

Install

In Claude Code you can also add the marketplace with /plugin marketplace add KalarisLabs/research-agent-skills and install the whole life-sciences category with /plugin install life-sciences@research-agent-skills.

Full playbook

Read SKILL.md for the complete workflow, references and any scripts. The agent installer copies the full skill folder.
Last modified on October 19, 2026