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Updated: Feb 14, 2026

Using an Automated Cell Counter to Simplify Gene Expression Studies: siRNA Knockdown of IL-4 Dependent Gene Expression in Namalwa Cells
Published on: April 14, 2010
SCANPY: large-scale single-cell gene expression data analysis
F Alexander Wolf1, Philipp Angerer2, Fabian J Theis3,4
1Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Munich, Neuherberg, Germany. alex.wolf@helmholtz-muenchen.de.
Abstract:
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 ( https://github.com/theislab/Scanpy ). Along with SCANPY, we present ANNDATA, a generic class for handling annotated data matrices ( https://github.com/theislab/anndata ).
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