Description
scanpy is an agent skill for single-cell RNA-seq analysis with Scanpy, a Python toolkit built on AnnData. It covers quality control, normalisation, highly variable gene selection, dimensionality reduction with PCA, UMAP and t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualisation and trajectory analysis. The skill targets Scanpy 1.12.4, released on 27 August 2026 and reviewed on 1 October 2026. The native synthetic tests check data and API contracts, but they do not establish biological validity. Scanpy 1.12 requires Python 3.12 or newer and AnnData 0.10 or later. The leiden extra installs igraph and leidenalg, and the scripts select the igraph flavour explicitly. For reproducible environments the skill recommends pinning the version. For large or out-of-memory datasets, many functions support Dask arrays, which the skill notes is experimental. Use it for a complete single-cell workflow, from raw counts to clusters and marker genes. It is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars. The listing shows it as free, and it has about 1,800 installs.…
Highlights
- QC, normalisation and HVG selection
- PCA, UMAP and t-SNE
- Clustering and marker ranking
- Pseudobulk preparation
- Targets Scanpy 1.12.4
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scanpy FAQ
What does Scanpy cover?
Single-cell RNA-seq workflows: quality control, normalisation, dimensionality reduction, clustering, marker genes, plotting and trajectories.
Do the tests show the results are biologically valid?
No. The skill says the native synthetic tests check data and API contracts, not biological validity.
Which Python version is needed?
Python 3.12 or newer, for Scanpy 1.12.
Does it handle large datasets?
Many functions support Dask arrays, which the skill describes as experimental.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill scanpy.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub and Socket, and a warning from Snyk.
What are the best scanpy alternatives?
Popular alternatives to scanpy include anndata, arboreto and scvelo. See all scanpy alternatives