bulk-rnaseq

What problem does it solve?

Bulk RNA-seq studies often break down when analysis steps are scattered, counts are assembled incorrectly, or experimental design and quality control are skipped. This Skill gives you a defensible path from raw reads or quantification output to differential expression, enrichment, and publication-ready figures.

Core Features & Use Cases

• Routes between nf-core/rnaseq and a standalone STAR, Salmon, or featureCounts workflow.
• Validates samplesheets and metadata for replicates, strandedness, and batch confounding before expensive analysis.
• Builds gene-level count matrices and prepares handoff files for downstream differential expression and enrichment tools.
• Use it when you need an end-to-end bulk RNA-seq analysis, want to sanity-check study design, or need counts ready for PyDESeq2 and pathway enrichment.

Quick Start

Use the bulk-rnaseq skill to validate your samplesheet and metadata, then choose the nf-core or standalone path to take your RNA-seq data from FASTQ files or quantification output through counts, differential expression, enrichment, and figures.