Single-Cell Analysis in Python.

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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 data sets of more than one million cells and enables easy integration of advanced machine learning algorithms.

Read the documentation. Learn more about conceptual ideas in our preprint.

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