Scanpy - Single-Cell Analysis

Scanpy processes high-dimensional biological data, reducing it via PCA/UMAP to identify rare cell populations in tissues or microbiomes.

When to Use

• Analyzing single-cell RNA sequencing (scRNA-seq) data.
• Identifying cell types and states in heterogeneous tissues.
• Reconstructing developmental trajectories.
• Comparing cell populations between conditions.
• Discovering rare cell types.

Core Principles

AnnData Format

Scanpy uses AnnData objects that store expression matrix, cell metadata, and gene annotations together.

Dimensionality Reduction