GeneNetwork (GN) is a free and open source (FOSS) framework for web-based genetics that can be deployed anywhere. GN allows biologists to upload high-throughput experimental data, such as expression data from microarrays and RNA-seq, and also `classic' phenotypes, such as disease phenotypes. These phenotypes can be mapped interactively against genotypes using embedded tools, such as R/QTL (Arends et al. 2010) mapping, interval mapping for model organisms and pylmm; an implementation of FaST-LMM (Lippert et al. 2011) which is more suitable for human populations and outbred crosses, such as the mouse diversity outcross. Interactive D3 graphics are included from R/qtlcharts and presentation-ready figures can be generated. Recently we have added functionality for phenotype correlation (Wang et al. 2016) and network analysis (Langfelder and Horvath 2008).
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