bulk-rnaseq

Editorial and source context

What this Skill does

Bulk Rnaseq is a source-indexed Agent Skill for design & frontend work. Based on the SKILL.md description, it focuses on end-to-end bulk rna-seq orchestrator — takes raw fastq reads through qc and trimming (fastqc,…. Use the linked GitHub file to confirm scope and prerequisites before enabling it.

What the author says

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.

Compatibility and requirements

• Use an agent runtime that supports Agent Skills and the linked SKILL.md format.
• Confirm the source repository's tools, SDKs, and platform prerequisites for ui and frontend work.

How to install or import it

• Open the linked GitHub SKILL.md and review its scope and setup instructions.
• Install or import the skill using the agent runtime's documented workflow.
• Run a small, non-sensitive test and verify the output before broader use.

Permissions and risks

• Review every command, file path, network request, dependency, and credential scope before enabling it.
• GitHub stars indicate popularity, not safety or correctness; validate the source and test with non-sensitive data.

Example workflows

• Ask an AI agent to apply Bulk Rnaseq to ui and frontend work described in the source record.
• Have the agent state assumptions, required tools, and expected output before using this design & frontend skill.
• Compare the result with the linked GitHub SKILL.md and verify it against your project requirements.