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"It's about analyzing gene-expression data of a large number of individual cells," explains lead author Alex Wolf of the Institute of Computational Biology (ICB) at Helmholtz Zentrum München. He developed Scanpy together with his colleague Philipp Angerer in the Machine Learning Group of Prof. Dr. Dr. Fabian Theis. In addition to his position at Helmholtz Zentrum, Theis is also a professor of mathematical modelling of biological systems at the Technical University of Munich. "New technical advances generate several orders of magnitude more data with a correspondingly greater information content," Theis says. "However, the historically evolved software infrastructure for gene-expression analysis simply wasn't designed to cope with the new challenges. New analytic methods are therefore needed."
According to Theis, a major international research project could also benefit from the software. A team of international scientists is compiling a reference database, called the Human Cell Atlas, which holds data on the gene activity of all human cell types. "For this project, and in a growing number of other projects in which databases are combined, it is important to have scalable software," says Theis. It is therefore no surprise that Scanpy...
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