GeneNetwork: framework for web-based genetics

Zachary Sloan; Danny Arends; Karl W. Broman; Arthur Centeno; Nicholas Furlotte; H. Nijveen; Lei Yan; Xiang  Zhou; Robert W. Williams; Pjotr Prins

doi:10.21105/joss.00025

GeneNetwork: framework for web-based genetics

Zachary Sloan, Danny Arends, Karl W. Broman, Arthur Centeno, Nicholas Furlotte, H. Nijveen, Lei Yan, Xiang Zhou, Robert W. Williams, Pjotr Prins

Bioinformatics (BIF)

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

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).

Original language	English
Article number	25
Number of pages	3
Journal	The Journal of Open Source Software
Volume	1
Issue number	2
DOIs	https://doi.org/10.21105/joss.00025
Publication status	Published - 29 May 2016

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title = "GeneNetwork: framework for web-based genetics",

abstract = "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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AU - Sloan, Zachary

AU - Arends, Danny

AU - Broman, Karl W.

AU - Centeno, Arthur

AU - Furlotte, Nicholas

AU - Nijveen, H.

AU - Yan, Lei

AU - Zhou, Xiang

AU - Williams, Robert W.

AU - Prins, Pjotr

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AB - 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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GeneNetwork: framework for web-based genetics

Abstract

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