title: CoNet app: inference of biological association networks using Cytoscape.
abstract: 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 briefly describe its main features and illustrate its use on microbial count data obtained by 16S rDNA sequencing of arctic soil samples. The CoNet app is available at: http://apps.cytoscape.org/apps/conet.
authors.affiliation: Center for the Biology of Disease, VIB, Leuven, 3000, Belgium; Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, VUB, Brussel, 1050, Belgium; Department of Microbiology and Immunology, REGA Institute, KU Leuven, 3000, Belgium.
authors.forename: Karoline
authors.initials: K
authors.lastname: Faust
authors.affiliation: Center for the Biology of Disease, VIB, Leuven, 3000, Belgium; Department of Microbiology and Immunology, REGA Institute, KU Leuven, 3000, Belgium.
authors.forename: Jeroen
authors.initials: J
authors.lastname: Raes
keywords: CoNet; Cytoscape; association networks; microbial networks; network construction; network generation; network inference