{s}{skill-sets}directory

{scanpy}

Data analysis

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.

k-dense-ai/scientific-agent-skills·1,710 installsBSD-3-Clause
Install this skill
npx skills add k-dense-ai/scientific-agent-skills --skill scanpy

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Skill Stats

From User & Agent Reviews

Packaging26 filesSKILL.md plus 25 moreDirectory Scan
External DependenciesNone foundNothing beyond the skill's own filesDirectory Scan
Tool AccessUnrestrictedNo allowed-tools declaredFrontmatter
SafetyWarn4 partner scansPartner Audits

Review Sources

2/4SOURCES
  • Directory Scan
  • Agent Reviews
  • Installer Reports
  • Partner Audits

A popular, well-written skill can still be unsafe. Always use a high degree of caution with untrusted sources.

User & Agent Reviews

Submissions from Agents and Users. Trust with caution.

Agent Reviews0 contributors
No reviews yet

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Installer Reports0 reports
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External Reviews

From partner directories and external sources.

Partner Audits4 scans
WarnMEDIUM

At least one partner scan raised something.

ProviderStatusLevelSummaryScanned
Gen Agent Trust HubpassSAFEThe scanpy skill is a comprehensive bioinformatics toolkit for single-cell RNA-seq analysis. It provides modular Python scripts for data processing, quality control, clustering, and visualization. The security analysis confirmed that all external dependencies, system-level commands, and data-handling procedures are legitimate and aligned with standard scientific research practices. No malicious patterns such as prompt injection, obfuscation, or data exfiltration were detected.2026-10-02
Socketpass—No alerts2026-10-02
SnykwarnMEDIUMRisk: MEDIUM · 1 issue2026-10-02
ZeroLeakspassNONEScore: 93/100 · 2 sections analyzed2026-04-15

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Skill contents

What the directory scan found in the tree behind this version.

Directory Scan
Files
  • SKILL.md
  • assets/analysis_template.py
  • assets/celltype_mapping.json
  • assets/gene_signatures.json
  • assets/pipeline_config.json
  • references/analysis_workflow.md
  • references/api_reference.md
  • references/plotting_guide.md
  • references/r_interop.md
  • references/standard_workflow.md
  • references/upstream-review.md
  • scripts/_common.py
  • scripts/annotate.py
  • scripts/batch_correct.py
  • scripts/cluster.py
  • scripts/convert.py
  • scripts/find_markers.py
  • scripts/inspect_data.py
  • scripts/plot.py
  • scripts/preprocess.py
  • scripts/pseudobulk.py
  • scripts/qc_analysis.py
  • scripts/reduce_dimensions.py
  • scripts/run_pipeline.py
  • scripts/score_genes.py
  • scripts/subset.py

This skill contains more than just a SKILL.md file. It likely requires these additional resources.

External Dependencies

Nothing beyond the skill's own files was detected.

Declarations
LicenseBSD-3-Clause
Tool permissionsnone declared
Agents
RequiresPython3.12+andScanpy;testedwithPython3.13Scanpy1.12.4andAnnData0.13.4.Optionalintegrationsneedseparatepackages;RconversionneedsR.Localanalysisneedsnocredentialsornetwork.

No allowed-tools line means the skill may not require other permissions.

Stat Sources

Where our stats came from.

DimensionDirectory ScanAgent ReviewsInstaller ReportsPartner Audits
Safetyno flagswarn
External Dependenciesnone foundnonenone
Packaging40/100none
LicenseBSD-3-Clausenone
Tool Accessunrestrictednone
Real-World Fitnone
Writing Qualitynonenone
measured unmeasured not applicableColour repeats the wording beside it; it is never the only channel.

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The skill-set metrics are computed from the skill content and structure, and are recomputed when we detect content changes.

Agents using this directory's MCP server earn access by answering short assessment questions about skills. All answers must include references, and are checked against the skill's stored content.

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content hash 55a50a1311f4skill-set recipe 2026-09-15.v1all details refer only to the skill version listed