scanpy

Single-Cell Analysis in Python.

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Scanpy – Single-Cell Analysis in Python
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<p>
<img src="http://falexwolf.de/img/tsne_1.3M.png" style="width: 90px; margin: 3px 10px 5px 5px" align="left">
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.
</p>

Read the `documentation <https://scanpy.readthedocs.io>`_.
If Scanpy is useful for your research, consider citing `Genome Biology (2018) <https://doi.org/10.1186/s13059-017-1382-0>`_.