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Paper: addressing openjournals/joss-reviews#25
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1st par: "experimental data" could be fleshed out in 2-3 words for the biologist reader (is it SNPs, microarray data, NGS, Y2H or manually counted individuals?)
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pjotrp committed Jun 2, 2016
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GeneNetwork (GN) is a free and open source (FOSS) framework for
web-based genetics that can be deployed anywhere. GN allows biologists
to upload experimental data and map phenotypes interactively against
genotypes using tools, such as R/QTL [@Arends:2010] mapping, interval
mapping for model organisms and pylmm; an implementation of FaST-LMM
[@Lippert:2011] which is 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:2016] and network analysis [@WGCNA:2008].
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:2010]
mapping, interval mapping for model organisms and pylmm; an
implementation of FaST-LMM [@Lippert: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:2016] and network
analysis [@WGCNA:2008].

-![Mouse LMM mapping example](qtl2.png)

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