Agent skill · research science · aiskillstore
deeptools
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
Why this skill is useful
Provides specific commands and workflows for NGS data analysis that the AI wouldn't reliably generate on its own.
What it needs
Requires deeptools installed locally. About 9k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
deepTools: NGS Data Analysis Toolkit Overview deepTools is a comprehensive suite of Python command-line tools designed for processing and analyzing high-throughput sequencing data. Use deepTools to perform quality control, normalize data, compare samples, and generate publication-quality visualizations for ChIP-seq, RNA-seq, ATAC-seq, MNase-seq, and other NGS experiments. Core capabilities: Convert BAM alignments to normalized coverage tracks (bigWig/bedGraph) Quality control assessment (fingerprint, correlation, coverage) Sample comparison and correlation analysis Heatmap and profile plot generation around genomic features Enrichment analysis and peak region visualization When to Use This Skill This skill should be used when: File conversion: "Convert BAM to bigWig", "generate coverage tracks", "normalize ChIP-seq data" Quality control: "check ChIP quality", "compare replicates", "assess sequencing depth", "QC analysis" Visualization: "create heatmap around TSS", "plot ChIP signal", "visualize enrichment", "generate profile plot" Sample comparison: "compare treatment vs control", "correlate samples", "PCA analysis" Analysis workflows: "analyze ChIP-seq data", "RNA-seq coverage", "ATAC-seq analysis", "complete workflow" Working with specific file types: BAM files, bigWig files, BED region files in genomics context Quick Start For users new to deepTools, start with file validation and common workflows: 1. Validate Input Files Before running any analysis, validate BAM, bigWig, and BED files using the validation script: This checks file existence, BAM indices, and format correctness. 2. Generate Workflow Template For standard analyses, use the workflow generator to create customized scripts: 3. Most Common Operations See assets/quickreference.md for frequently used commands and parameters. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/deeptools--1874c0