deeptools
No security findings. Scanned 1 time, most recently 2026-10-21.
Second scanner: NVIDIA SkillSpector
Independent static run, no language model, over the same files as the Cisco scan above. How the two scanners compare across the whole corpus: Two scanners, one corpus.
What this skill does
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
- Package
- 10 files, 105 KB
- SKILL.md
- 2255 words, 12+ sections
- Code
- Python (2)
- Allowed tools
ReadWriteEditBash- License
- BSD license
- Compatibility
- Requires Python 3.12+ and deepTools 4.0.0 (including pysam and pyBigWig); samtools for sorting/indexing workflows. Network needed only for installation or retrieving public input data.
SKILL.md covers: deepTools: NGS Data Analysis Toolkit · Overview · When to Use This Skill · Quick Start · 1. Validate Input Files · 2. Generate Workflow Template · List available workflows · Generate ChIP-seq QC workflow · Make executable and run · 3. Most Common Operations · Installation · Core Workflows and Tool Categories
Findings
No findings. SAFE
What is in the package
| File | Kind | Size |
|---|---|---|
SKILL.md | doc | 18 KB |
assets/quick_reference.md | doc | 2.1 KB |
references/core_workflows.md | doc | 4.6 KB |
references/effective_genome_sizes.md | doc | 3.5 KB |
references/normalization_methods.md | doc | 7.6 KB |
references/review.md | doc | 6.3 KB |
references/tools_reference.md | doc | 24 KB |
references/workflows.md | doc | 12 KB |
scripts/validate_files.py | script | 9.8 KB |
scripts/workflow_generator.py | script | 18 KB |
External hosts referenced
deeptools.readthedocs.io github.com arxiv.org doi.org export.arxiv.org pypi.org pysam.readthedocs.io
Hostnames that appear in the skill's files. Referencing a host is not a finding; compare against the findings above and the skill's stated purpose.
Environment variables referenced
OUTPUT_DIR
Package contents recorded 2026-10-22 at commit 593377bb0487. The scan above ran against the version current at scan time; the two can differ if the skill has since been updated.
What we checked
- Static analyzer. Pattern rules over SKILL.md and bundled files: known-bad commands, exfiltration URLs, secrets, obfuscation.
- Bytecode analyzer.
- Pipeline analyzer.
- Correlation analyzer.
- Behavioral analyzer. Checks what the skill asks the agent to do against what its description claims it does.
- Trigger analyzer. Looks for instructions that fire on conditions the user did not ask for.
What we did not check
- Runtime behaviour. The skill was not executed; findings come from reading its files.
- Anything fetched at install or run time, including remote scripts, package dependencies, and URLs the skill tells the agent to open.
- Content the analyzers cannot read: images, binaries, and some non-English text.
- Known scanner bypass classes. See the methodology and limitations page.
Sources
- Repository: https://github.com/K-Dense-AI/scientific-agent-skills
- Raw scan result: skills-deeptools-scan.json
- Badge for your README:
- Request a re-scan