Single-Cell Analysis in Python. Scales to >1M cells.
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README.rst

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Scanpy – Single-Cell Analysis in Python

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Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

Read the documentation. If Scanpy is useful for your research, consider citing Genome Biology (2018).