Deeptools

If you're working with ChIP-seq, RNA-seq, or ATAC-seq data, this wraps the deepTools Python toolkit for converting BAM files to normalized bigWig tracks, running quality control checks, and generating heatmaps around genomic features like TSS or peaks. The skill includes workflow generators that scaffold complete analysis pipelines (ChIP QC, coverage generation, visualization) and validation scripts to check your inputs before running long jobs. The normalization guidance is solid, it covers RPGC vs CPM vs RPKM clearly, and the fingerprint plots for assessing ChIP enrichment are genuinely useful. This is a workhorse toolkit if you're past alignment and need to actually look at your data.

Install to Claude Code

npx -y skills add k-dense-ai/scientific-agent-skills --skill deeptools --agent claude-code