deeptools
K-Dense-AI/scientific-agent-skills
deepTools is a comprehensive command-line toolkit for processing and analyzing high-throughput sequencing (NGS) data. It provides core capabilities for quality control (QC), data normalization, sample comparison, and generating publication-quality visualizations for various assays, including ChIP-seq, RNA-seq, and ATAC-seq. Use it for converting BAM files to bigWig tracks, performing PCA, and creating heatmaps around genomic features.