/scanpy

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

Primary LanguagePythonBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

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Scanpy – Single-Cell Analysis in Python

Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing and simulation of gene regulatory networks. 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).