BG
Data & Repro
bgpt-paper-search
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Data & Repro
DE
deepTools
Maintainer K-Dense Inc. · Last updated April 1, 2026
deepTools is a comprehensive suite of Python command-line tools designed for processing and analy.
Original source
K-Dense-AI/claude-scientific-skills
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/deeptools
- Maintainer
- K-Dense Inc.
- License
- BSD license
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- 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.
Source Doc
Excerpt From SKILL.md
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.
Use cases
- **File conversion**: "Convert BAM to bigWig", "generate coverage tracks", "normali.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
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