pydeseq2
No security findings. Scanned 1 time, most recently 2026-10-21.
Second scanner: NVIDIA SkillSpector
SkillSpector found no issues but could not fully inspect the package, usually because SKILL.md refers to a file that is not present, so it fails closed to CAUTION instead of SAFE. Read it as "not fully checked", not as a finding. How the two scanners compare across the whole corpus: Two scanners, one corpus.
What this skill does
Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests, FDR correction, coefficient-matched LFC shrinkage, and result visualization. Use for PyDESeq2 or Python DESeq2 workflows with biological replicates.
- Package
- 6 files, 54 KB
- SKILL.md
- 1273 words, 7 sections
- Code
- Python (1)
- Allowed tools
ReadWriteEditBash- License
- MIT license
- Compatibility
- Requires Python >=3.11 and PyDESeq2 0.5.4. Tested current stack uses Python 3.13 and AnnData 0.13.4 (which requires Python >=3.12). Local analyses need no credentials or network; installation and upstream example-data downloads need network access.
SKILL.md covers: PyDESeq2 · Analysis contract · Quick start · Statistical interpretation · Normalization and shrinkage pitfalls · Detailed workflows · Citing Scientific Agent Skills
Findings
No findings. SAFE
What is in the package
| File | Kind | Size |
|---|---|---|
SKILL.md | doc | 10 KB |
references/analysis_patterns.md | doc | 5.1 KB |
references/api_reference.md | doc | 8.8 KB |
references/core_workflow_steps.md | doc | 3.4 KB |
references/workflow_guide.md | doc | 9.0 KB |
scripts/run_deseq2_analysis.py | script | 17 KB |
External hosts referenced
github.com pydeseq2.readthedocs.io arxiv.org bioconductor.org formulaic-contrasts.readthedocs.io doi.org export.arxiv.org pypi.org raw.githubusercontent.com
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.
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-pydeseq2-scan.json
- Badge for your README:
- Request a re-scan