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Here we present the Cytoscape app version of our association network inference tool CoNet. Though CoNet was developed with microbial community data from sequencing experiments in mind, it is designed to be generic and can detect associations in any data set where biological entities (such as genes, metabolites or species) have been observed repeatedly. The CoNet app supports Cytoscape 2.x and 3.x and offers a variety of network inference approaches, which can also be combined. Here we brieflydoi:10.12688/f1000research.9050.2 pmid:27853510 pmcid:PMC5089131 fatcat:7ssccmqldfhl5flgvqh5mmxoie