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. Current stable release: scanpy 1.12.x (January 2026).

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 python-igraph and leidenalg, required for Leiden clustering. For reproducible environments, pin a version: uv pip install "scanpy[leiden]==1.12.1".

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