---
title: "Scanpy: Single-Cell Analysis - Air Market"
description: "You have single-cell RNA-seq data and want to explore it along the well-trodden route: clean it, cluster it, see what differs. This covers that path end to end, and it will also bring data over from…"
canonical: "https://airmarket.ai/app/scanpy"
---

[Air Market](/) / [Data & Analytics](/category/data) / Scanpy: Single-Cell Analysis

Skill by [K-Dense](/@k-dense-ai)

# Scanpy: Single-Cell Analysis

Walk single-cell RNA-seq data through the usual analysis path

## What this does

You have single-cell RNA-seq data and want to explore it along the well-trodden route: clean it, cluster it, see what differs. This covers that path end to end, and it will also bring data over from R formats so you can start. Reach for it when the established workflow is what you want, not a new model.

### Top 3 things it does for you

- Run QC and normalization on scRNA-seq data
- Cluster cells and reduce dimensions with PCA, UMAP or t-SNE
- Test for differential expression and plot the result

## Information

**Scanpy: Single-Cell Analysis at a glance**

|  |  |
| --- | --- |
| Kind | Skill |
| Publisher | [K-Dense](/@k-dense-ai) |
| Category | [Data & Analytics](/category/data) |
| Works with | Agent Skills - an open standard supported by 40+ agents |
| Version | 1.5 |
| Size | 119 KB |
| Licence | MIT |
| Repository | [k-dense-ai/scientific-agent-skills](https://github.com/k-dense-ai/scientific-agent-skills/tree/0e451065e3308e9902d8229e17d2028359b2bbaf/skills/scanpy) |
| GitHub stars | 34,239 (as of Nov 2026) |

## Security report

**Verified.** AIR scanned this exact version of Scanpy: Single-Cell Analysis and flagged nothing. AIR's verdict: **safe**.

**What Scanpy: Single-Cell Analysis's check was run against**

|  |  |
| --- | --- |
| Commit | 0e451065e3308e9902d8229e17d2028359b2bbaf |
| Content hash | 8c8e612f47a4dcf0a77cccc2d24680554f54404958ce54efd3b9842e7fef3b93 |
| Files read | [Browse the files at this exact commit](https://github.com/k-dense-ai/scientific-agent-skills/blob/0e451065e3308e9902d8229e17d2028359b2bbaf/skills/scanpy/SKILL.md) |

A scan is named by the exact content it read, not by a version number. A different version is a different artifact, and nothing here applies to a version AIR has not scanned.

[Read the full security report for Scanpy: Single-Cell Analysis](/security/scanpy)

## About Scanpy: Single-Cell Analysis

A standard single-cell RNA-seq analysis pipeline. It spans quality control, normalization, dimensionality reduction with PCA, UMAP or t-SNE, clustering, differential expression and visualization.

It also handles getting data in from the R side, converting single-cell formats such as Seurat or SingleCellExperiment RDS files into h5ad.

It is best suited to exploratory scRNA-seq work with established workflows. For deep learning models the pointer is to scvi-tools, and for data format questions, to anndata.

## What's inside

- SKILL.md - instructions
- assets/analysis_template.py - script
- assets/celltype_mapping.json - data
- assets/gene_signatures.json - data
- assets/pipeline_config.json - data
- references/analysis_workflow.md - reference
- references/api_reference.md - reference
- references/plotting_guide.md - reference
- references/r_interop.md - reference
- references/standard_workflow.md - reference
- scripts/_common.py - script
- scripts/annotate.py - script
- scripts/batch_correct.py - script
- scripts/cluster.py - script
- scripts/convert.py - script
- scripts/find_markers.py - script
- scripts/inspect_data.py - script
- scripts/plot.py - script
- scripts/preprocess.py - script
- scripts/pseudobulk.py - script
- scripts/qc_analysis.py - script
- scripts/reduce_dimensions.py - script
- scripts/run_pipeline.py - script
- scripts/score_genes.py - script
- scripts/subset.py - script

## Questions

### Is Scanpy: Single-Cell Analysis safe to install?

AIR scanned this exact version of Scanpy: Single-Cell Analysis and flagged nothing. AIR's verdict: safe. The verdict is named by the content that was read, at commit 0e451065e330, so it cannot drift onto a version nobody scanned. The full report is at https://airmarket.ai/security/scanpy.

### How do I install Scanpy: Single-Cell Analysis?

Open https://airmarket.ai/app/scanpy on Air Market and use the install action: Air Market hands Claude a prompt naming this exact skill, and Claude sets it up. Source, pinned to the exact commit this listing describes: https://github.com/k-dense-ai/scientific-agent-skills/tree/0e451065e3308e9902d8229e17d2028359b2bbaf/skills/scanpy. Install from that link, not the branch.

## Related on Air Market

- [More Data & Analytics listings](/category/data)
- [Everything by K-Dense](/@k-dense-ai)

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Canonical URL: <https://airmarket.ai/app/scanpy>