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scanpy
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580
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Single-cell analysis in Python. Scales to >1M cells.
scvi-tools
1.1k
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342
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Deep probabilistic analysis of single-cell and spatial omics data
squidpy
398
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71
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Spatial Single Cell Analysis in Python
muon
200
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28
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muon is a multimodal omics Python framework
anndata
509
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148
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Annotated data.
mudata
68
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16
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Multimodal Data (.h5mu) implementation for Python