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bioRxiv · 10.1101/2024.11.22.624823

NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks

Paton, V.·Turei, D.·Ivanova, O.·Muller-Dott, S.·Rodriguez-Mier, P.·Venafra, V.·Perfetto, L.·Garrido-Rodriguez, M.·Saez-Rodriguez, J.
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Abstract

SummaryWe present NetworkCommons, a platform for integrating prior knowledge, omics data, and network inference methods, facilitating their usage and evaluation. NetworkCommons aims to be an infrastructure for the network biology community that supports the development of better methods and benchmarks, by enhancing interoperability and integration. Availability and ImplementationNetworkCommons is implemented in Python and offers programmatic access to multiple omics datasets, network inference methods, and benchmarking setups. It is a free software, available at https://github.com/saezlab/networkcommons. Contactsaezlab@ebi.ac.uk, martin.garrido@embl.de Supplementary DataContribution guidelines, additional figures, and descriptions for data, knowledge, methods, evaluation strategies and their implementation are available in the Supplementary Data and in the NetworkCommons documentation at https://networkcommons.readthedocs.io/.

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Paton, V., Turei, D., Ivanova, O., Muller-Dott, S., Rodriguez-Mier, P., Venafra, V., Perfetto, L., Garrido-Rodriguez, M., Saez-Rodriguez, J.. 2024-11-25. NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks. https://doi.org/10.1101/2024.11.22.624823

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