scanpy
Analyze Single-Cell RNA-Seq with Scanpy
Single-cell RNA-seq workflows require careful QC, normalization, clustering, and documentation. This skill gives Scanpy workflows, scripts, templates, and references for reproducible analysis.
Install with my Agent
Copy this request to your Agent. It includes the canonical Skill page and manifest.
Review the Skillstore skill "scanpy" from https://skillstore.io/skills/davila7-scanpy.md and its manifest at https://skillstore.io/api/skills/davila7-scanpy/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.Your Agent should still show its plan and request any confirmation required by the security policy.
Agent-readable resources
Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.
Test it
Using "scanpy". User asks for QC on a PBMC h5ad file.
Expected outcome:
The response lists QC metrics, plot names, threshold ranges, filtering steps, and saved filtered data outputs.
Using "scanpy". User asks how to annotate clusters.
Expected outcome:
The response recommends marker genes, dot plots, UMAP checks, a cluster-to-cell-type table, and validation notes.
Using "scanpy". User asks for publication figures.
Expected outcome:
The response proposes UMAP, heatmap, dot plot, violin plot, and export settings for figure-ready files.
Security Audit
SafeThe flagged Ruby or shell execution patterns are Markdown code fences, inline documentation, or user-run examples. The filesystem and network findings are expected local output creation and public documentation links.
Risk Factors
📁 Filesystem access (2)
⚙️ External commands (50)
🌐 Network access (3)
Share & cite this report
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https://skillstore.io/skills/davila7-scanpy/audits/9?utm_source=security_passport&utm_medium=share&utm_campaign=versioned_reportMarkdown badge
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<a href="https://skillstore.io/skills/davila7-scanpy?utm_source=security_passport_badge"><img src="https://skillstore.io/badges/skills/davila7-scanpy/security.svg" alt="Skillstore security assessment" loading="lazy"></a>Embed card
<iframe src="https://skillstore.io/embed/skills/davila7-scanpy.html" title="Skillstore Security Assessment" sandbox="allow-popups allow-popups-to-escape-sandbox" loading="lazy" referrerpolicy="no-referrer" width="420" height="180"></iframe>Academic citations (APA · BibTeX · CFF)
APA citation
davila7. (2026). scanpy security audit report (audit version 9) [Author version unspecified]. Skillstore. https://skillstore.io/skills/davila7-scanpy/audits/9BibTeX citation
@techreport{davila7-davila7-scanpy-2026,
author = {davila7},
title = {scanpy security audit report (audit version 9)},
institution = {Skillstore},
year = {2026},
number = {9},
url = {https://skillstore.io/skills/davila7-scanpy/audits/9},
note = {Author version unspecified}
}CITATION.cff
cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "scanpy security audit report (audit version 9)"
version: "unspecified"
type: report
authors:
- name: "davila7"
date-released: "2026-07-23"
url: "https://skillstore.io/skills/davila7-scanpy/audits/9"
identifiers:
- type: other
value: "skillstore:davila7-scanpy:audit:9"
description: "Skillstore immutable audit report identifier"
Compare variants
2 installable variantsEach author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.
Why this variant is first
davila7-scanpy
2026-08-21
k-dense-ai-scanpy
2026-08-21
Skillstore Score
Why this score Evidence Confidence: HighWhat You Can Build
Run Initial Dataset QC
Run quality control and clustering on a new 10X or h5ad dataset.
Build Reproducible Workflows
Create a Scanpy workflow with saved outputs and documented parameters.
Prepare Analysis Figures
Compare markers, trajectories, and condition effects before preparing figures.
Try These Prompts
Use the Scanpy skill to plan QC for my h5ad file. Include metrics, thresholds, plots, and expected outputs.
Create a Scanpy workflow for loading 10X data, normalizing cells, clustering, and saving results. Explain each analysis choice.
Review my Scanpy results and suggest clustering resolutions, PCA dimensions, and neighbor settings to test next. Include validation checks.
Design an advanced Scanpy analysis plan with marker ranking, annotation validation, differential expression, trajectory checks, and publication figures.
Best Practices
- Save raw counts before filtering genes.
- Adjust QC thresholds from dataset-specific plots.
- Validate annotations with multiple marker genes.
Avoid
- Do not reuse thresholds without checking data quality.
- Do not treat cluster numbers as biological labels.
- Do not skip intermediate outputs for long workflows.
Frequently Asked Questions
What data formats does it support?
Can it run QC automatically?
Does it install Scanpy?
Can it annotate cell types?
Does it use network services?
Can it handle large datasets?
Developer Details
Author
davila7License
MIT
Skillstore revision
r1
Version notice
The author did not declare a version.
Ref
c43861a65bb95efcae259cd161c9d6f4dc7eec6f
Maintenance freshness
7/24/2026
Usage
13 downloads · 480 views
File structure