Liftoff.bio illustration — cat single cell

Scanpy

Scalable single-cell analysis in Python

Scanpy is the backbone of the Python single-cell ecosystem (scverse). Built on the AnnData structure, it scales to millions of cells.

Example

1import scanpy as sc
2adata = sc.read_h5ad("pbmc.h5ad")
3sc.pp.normalize_total(adata, target_sum=1e4)
4sc.pp.log1p(adata)
5sc.pp.pca(adata)
6sc.pp.neighbors(adata)
7sc.tl.leiden(adata)
8sc.pl.umap(adata, color="leiden")

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