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1. scanpy scanpy Public

   Single-cell analysis in Python. Scales to >100M cells.

   Python 2.1k 620

2. anndata anndata Public

   Annotated data.

   Python 613 161

3. muon muon Public

   muon is a multimodal omics Python framework

   Python 230 31

4. mudata mudata Public

   Multimodal Data (.h5mu) implementation for Python

   Python 91 19

5. scvi-tools scvi-tools Public

   Deep probabilistic analysis of single-cell and spatial omics data

   Python 1.4k 382

6. scirpy scirpy Public

   A scanpy extension to analyse single-cell TCR and BCR data.

   Python 227 38