deeptools
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
npx skills add K-Dense-AI/scientific-agent-skills --skill deeptools --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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 workflo
- Overview
- When to Use This Skill
- Quick Start
- 1. Validate Input Files
- 2. Generate Workflow Template
- 3. Most Common Operations
- Installation
- Core Workflows and Tool Categories
- Normalization Methods
- Effective Genome Sizes
- Common Parameters Across Tools
- Best Practices
- File Validation
- Analysis Strategy
python scripts/validate_files.py --bam sample1.bam sample2.bam --bed regions.bed List available workflows python scripts/workflow_generator.py --list Generate ChIP-seq QC workflow python scripts/workflow_generator.py chipseq_qc -o qc_workflow.sh \ Make executable and run chmod +x qc_workflow.sh uv pip install deepTools==3.5.6 conda install -c conda-forge -c bioconda deeptools samtools index input.bam
What does the deeptools skill do?
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
How do I install it?
Run `npx skills add K-Dense-AI/scientific-agent-skills --skill deeptools --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From K-Dense-AI/scientific-agent-skills, a repository with 32,619 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.