Deeptools

If you're working with ChIP-seq, RNA-seq, or ATAC-seq data, this handles the standard pipeline from BAM files to publication-ready visualizations. It wraps the deepTools Python suite with workflow generators for common tasks like converting alignments to normalized bigWig tracks, running QC checks (fingerprint plots, sample correlation, PCA), and creating heatmaps around genomic features like TSSs or peaks. The skill includes validation scripts and templates for complete workflows, which is helpful since deepTools has a lot of normalization options (RPGC, CPM, RPKM) and it's easy to pick the wrong one. The quick reference and workflow documentation actually explain when to use what, which beats hunting through the official docs.