scanpy
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
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