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scanpy

k-dense-ai/scie…t-skills

Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or SingleCellExperiment RDS conversion to h5ad. Applies to established exploratory scRNA-seq workflows with explicit count and expression provenance; complementary skills cover scvi-tools models and AnnData format details.

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安装命令

npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill scanpy

SKILL.md

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. Targets Scanpy 1.12.4 (released 2026-08-27), reviewed 2026-10-01. Native synthetic tests establish data/API contracts, not biological validity.

Installation

Requires Python 3.12+ (scanpy 1.12 dropped Python ≤3.11) and anndata ≥0.10.

uv pip install "scanpy[leiden]"

The [leiden] extra installs igraph and leidenalg; the scripts explicitly select flavor="igraph". For reproducible environments, pin a version: uv pip install "scanpy[leiden]==1.12.4".

For large or out-of-core datasets, many functions support Dask arrays (experimental):

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