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Scanpy 2.0

Project Scanpy

Fabian Theis (Helmholtz Zentrum Munich)

Funding Cycle 1

Proposal Summary

To expand Scanpy’s core infrastructure and community platforms for stability, versatility, and sharing knowledge.



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

Key Personnel

Fabian Theis
Alex Wolf
Phillipp Angerer