PuSH - Publication Server of Helmholtz Zentrum München: Correlation-guided Network Integration (CoNI), an R package for integrating numerical omics data that allows multiform graph representations to study molecular interaction networks.

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Monroy Kuhn, J.M. ; Miok, V. ; Lutter, D.

Correlation-guided Network Integration (CoNI), an R package for integrating numerical omics data that allows multiform graph representations to study molecular interaction networks.

Bioinfo. Adv. 2:vbac042 (2022)

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SUMMARY: Today's immense growth in complex biological data demands effective and flexible tools for integration, analysis and extraction of valuable insights. Here, we present CoNI, a practical R package for the unsupervised integration of numerical omics datasets. Our tool is based on partial correlations to identify putative confounding variables for a set of paired dependent variables. CoNI combines two omics datasets in an integrated, complex hypergraph-like network, represented as a weighted undirected graph, a bipartite graph, or a hypergraph structure. These network representations form a basis for multiple further analyses, such as identifying priority candidates of biological importance or comparing network structures dependent on different conditions. AVAILABILITY AND IMPLEMENTATION: The R package CoNI is available on the Comprehensive R Archive Network (https://cran.r-project.org/web/packages/CoNI/) and GitLab (https://gitlab.com/computational-discovery-research/coni). It is distributed under the GNU General Public License (version 3). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.

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