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 . The extra installs and ; the scri…