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. 2013 Jul 15;29(14):1830-1.
doi: 10.1093/bioinformatics/btt285. Epub 2013 Jun 4.

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

Weijun Luo  1 , Cory Brouwer
Affiliations

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

Weijun Luo et al. Bioinformatics. .

Abstract

Summary: Pathview is a novel tool set for pathway-based data integration and visualization. It maps and renders user data on relevant pathway graphs. Users only need to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps and integrates user data onto the pathway and renders pathway graphs with the mapped data. Although built as a stand-alone program, Pathview may seamlessly integrate with pathway and functional analysis tools for large-scale and fully automated analysis pipelines.

Availability: The package is freely available under the GPLv3 license through Bioconductor and R-Forge. It is available at http://bioconductor.org/packages/release/bioc/html/pathview.html and at http://Pathview.r-forge.r-project.org/.

Contact: luo_weijun@yahoo.com

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Example Pathview graphs: (a) Graphviz view on a canonical signaling pathway (hsa04110 Cell cycle) with gene data only, (b) KEGG view on a metabolic pathway (hsa00640 Propanoate metabolism) with both discrete gene data and continuous metabolite data integrated. The same graphs at a higher resolution or with a different color scheme are shown in Supplementary Figures S3 and S4
See this image and copyright information in PMC

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