bulk-rnaseq
K-Dense-AI/scientific-agent-skills
This skill provides an end-to-end, highly reproducible workflow for bulk RNA-seq differential expression analysis. It orchestrates the entire pipeline, guiding users from raw FASTQ reads through Quality Control (QC), trimming, alignment (STAR/Salmon), quantification, generating a gene-level counts matrix, and finally executing differential expression testing (pydeseq2) and pathway enrichment analysis. It is designed for robust, statistically sound, and fully documented results.