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1. scanpy scanpy Public

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

   Python 2.1k 638

2. anndata anndata Public

   Annotated data.

   Python 626 164

3. scvi-tools scvi-tools Public

   Deep probabilistic analysis of single-cell and spatial omics data

   Python 1.4k 390

4. squidpy squidpy Public

   Spatial Single Cell Analysis in Python

   Python 489 96

5. spatialdata spatialdata Public

   An open and interoperable data framework for spatial omics data

   Python 283 61

6. scirpy scirpy Public

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

   Python 231 37