bulk-rnaseq

SUMMARY

What it does

This skill orchestrates a complete bulk RNA-seq differential-expression workflow, from raw FASTQ reads through QC, trimming, alignment, and quantification to a gene-level counts matrix, then hands off to downstream skills for differential expression, pathway enrichment, and figure generation. It supports both an nf-core/rnaseq (Nextflow) path and a standalone STAR/Salmon path, and includes guidance on experimental design and QC. The skill is intended for users with bulk RNA-seq data who want a reproducible analysis; for single-cell data, the scanpy skill should be used instead.