Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression. Covers nf-core/rnaseq and standalone quantification, biological replication, strandedness, reference provenance, validated count assembly and a PyDESeq2 handoff. Use for FASTQ-to-counts analysis, nf-core/rnaseq configuration, STAR/Salmon quantification, or building a counts matrix for DESeq2.
Install
npx skills add K-Dense-AI/scientific-agent-skills --skill bulk-rnaseqnpx skills add K-Dense-AI/scientific-agent-skills --skill bulk-rnaseq -a claude-code -gnpx skills add K-Dense-AI/scientific-agent-skills --skill bulk-rnaseq -a codex -ggemini skills install https://github.com/K-Dense-AI/scientific-agent-skills.git --path skills/bulk-rnaseqgh skill install K-Dense-AI/scientific-agent-skills bulk-rnaseqgit clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills /tmp/K-Dense-AI__scientific-agent-skills
mkdir -p ~/.claude/skills ~/.agents/skills
cp -R /tmp/K-Dense-AI__scientific-agent-skills/skills/bulk-rnaseq ~/.claude/skills/bulk-rnaseq # Claude Code
cp -R /tmp/K-Dense-AI__scientific-agent-skills/skills/bulk-rnaseq ~/.agents/skills/bulk-rnaseq # Codex, Cursor, Gemini CLI, Copilot, OpenCode