Individual skill
scanpy
Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.
cli-tool/components/skills/scientific/scanpy/SKILL.md
Source commit ad81bf053f80b626801decf425f501ba49983d98
What was checked
- Matches the observed repository HEAD
- Yes
- Scanner rules are current
- No
- Repository scan complete
- No
- Skill scan complete
- No
- Observed behavior
- Not checked yet
- Last checked
- Nov 4, 2026
These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.
Install this skill
Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.
An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.
Repository context
- Repository stars (not skill ratings)
- 33,211
- Repository last updated
- Nov 8, 2026
- License
- MIT
Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.
- anthropic Repository topic
- anthropic-claude Repository topic
- claude Repository topic
- claude-code Repository topic
- agent-skills Repository topic
- ai-agents Repository topic
- claude-code-plugins Repository topic
- cli Repository topic
- mcp Repository topic
- registry Repository topic
- data Derived category
Files and excerpt
File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.
Browse files
SKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesSKILL.mdcore · 11,109 bytesassets/analysis_template.pyruns · 9,515 bytesreferences/api_reference.mddoc · 7,415 bytesreferences/plotting_guide.mddoc · 9,695 bytesreferences/standard_workflow.mddoc · 5,529 bytesscripts/qc_analysis.pyruns · 6,706 bytes
Read excerpt
# Scanpy: Single-Cell Analysis
## Overview
Scanpy is a scalable Python toolkit for analyzing single-cell RNA-seq data, built on AnnData. Apply this skill for complete single-cell workflows including quality control, normalization, dimensionality reduction, clustering, marker gene identification, visualization, and trajectory analysis.
## When to Use This Skill
This skill should be used when:
- Analyzing single-cell RNA-seq data (.h5ad, 10X, CSV formats)
- Performing quality control on scRNA-seq datasets
- Creating UMAP, t-SNE, or PCA visualizations
- Identifying cell clusters and finding marker genes
- Annotating cell types based on gene expression