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1. scanpy scanpy Public

   Single-cell analysis in Python. Scales to >1M cells.

   Python 1.9k 600

2. anndata anndata Public

   Annotated data.

   Python 577 153

3. muon muon Public

   muon is a multimodal omics Python framework

   Python 218 31

4. mudata mudata Public

   Multimodal Data (.h5mu) implementation for Python

   Python 77 17

5. scvi-tools scvi-tools Public

   Deep probabilistic analysis of single-cell and spatial omics data

   Python 1.2k 350

6. scirpy scirpy Public

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

   Python 219 34