scanpy

What problem does it solve?

Scanpy provides an end-to-end workflow for analyzing single-cell RNA-seq data, from QC to trajectory analysis, using the AnnData data structure and a comprehensive set of preprocessing and visualization tools.

Core Features & Use Cases

• QC, normalization, HVG selection, and scaling
• Dimensionality reduction (PCA/UMAP/TSNE) and neighborhood graphs
• Clustering (Leiden/Louvain) and marker gene identification
• Cell type annotation, trajectory inference, and plotting
• Integration with Muon for multi-modal data and scverse ecosystem

Use cases include single-cell data exploration, publishing-quality plots, and reproducible scRNA-seq pipelines.

Quick Start

Load an h5ad dataset, run QC, normalization, HVG selection, PCA and UMAP, then cluster and annotate.