scanpy
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
Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or SingleCellExperiment RDS conversion to h5ad. Applies to established exploratory scRNA-seq workflows with explicit count and expression provenance; complementary skills cover scvi-tools models and AnnData format details.
- Package
- 26 files, 148 KB
- SKILL.md
- 2456 words, 12+ sections
- Code
- Python (16)
- License
- BSD-3-Clause
- Compatibility
- Requires Python 3.12+ and Scanpy; tested with Python 3.13, Scanpy 1.12.4, and AnnData 0.13.4. Optional integrations need separate packages; R conversion needs R. Local analysis needs no credentials or network.
SKILL.md covers: Scanpy: Single-Cell Analysis · Overview · Installation · Representation and inference contracts · When to Use This Skill · Script Toolkit (prefer these over writing code from scratch) · One-shot end-to-end run · Counts → clustered object and exploratory marker ranks + figures + marker CSVs · With multi-sample integration: · Reproducible parameters via JSON (keys mirror flag names with underscores): · Step-by-step chain (when you need to inspect/iterate between stages) · inspect results/markers/*.csv, decide labels, write a mapping JSON, then:
Findings
No findings. SAFE
What is in the package
26 files, 148 KB. Show the list.
| File | Kind | Size |
|---|---|---|
SKILL.md | doc | 20 KB |
assets/analysis_template.py | script | 10.0 KB |
assets/celltype_mapping.json | config | 184 B |
assets/gene_signatures.json | config | 355 B |
assets/pipeline_config.json | config | 380 B |
references/analysis_workflow.md | doc | 7.6 KB |
references/api_reference.md | doc | 9.1 KB |
references/plotting_guide.md | doc | 10 KB |
references/r_interop.md | doc | 12 KB |
references/standard_workflow.md | doc | 7.0 KB |
references/upstream-review.md | doc | 8.3 KB |
scripts/_common.py | script | 10.0 KB |
scripts/annotate.py | script | 3.7 KB |
scripts/batch_correct.py | script | 3.1 KB |
scripts/cluster.py | script | 2.5 KB |
scripts/convert.py | script | 1.5 KB |
scripts/find_markers.py | script | 4.3 KB |
scripts/inspect_data.py | script | 3.1 KB |
scripts/plot.py | script | 3.6 KB |
scripts/preprocess.py | script | 3.5 KB |
scripts/pseudobulk.py | script | 4.6 KB |
scripts/qc_analysis.py | script | 5.1 KB |
scripts/reduce_dimensions.py | script | 2.8 KB |
scripts/run_pipeline.py | script | 9.4 KB |
scripts/score_genes.py | script | 3.9 KB |
scripts/subset.py | script | 2.6 KB |
External hosts referenced
scanpy.readthedocs.io github.com cloud.r-project.org scanpy.scverse.org cran.r-project.org mojaveazure.github.io www.bioconductor.org anndata.readthedocs.io arxiv.org satijalab.github.io docs.dask.org doi.org export.arxiv.org formulae.brew.sh mac.r-project.org rapids-singlecell.readthedocs.io satijalab.org scverse.org theislab.github.io www.r-project.org
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-scanpy-scan.json
- Badge for your README:
- Request a re-scan