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scanpy

Open source alternatives to scanpy

24 open source AI Skills apps to use instead, best rated first.

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About scanpy

S

scanpy

Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection

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.

View scanpyAll AI Skills apps
Price
Free
Made by
k-dense-ai
Category
AI Skills
Website
github.com/k-dense-ai/scientific-agent-skills/scanpy