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Luo Weijun ★ 1.5k@luo-weijun-1783
Last seen 10 weeks ago
Dear BioC users: The ISMB 2014 is at the corner. We will give two oral presentations introducing Pathview, a recently published tool for pathway-based data integration and visualization. If you are interested, below is the detail and abstract. We look forward to seeing you there. Thank you! Weijun Monday, July 14 11:00 - 11:25 am Room 309 John B. Hynes Memorial Convention Center, Boston, Massachusetts Technology Track [TT10] Pathview: an R/Bioconductor package for pathway-based data integration and visualization Saturday, July 12 10:45-11:03 am Room 203 John B. Hynes Memorial Convention Center, Boston, Massachusetts BOSC [Interoperability] Pathview: an R/Bioconductor Package for Pathway-based Data Integration and Visualization Pathview: an R/Bioconductor package for pathway-based data integration and visualization Weijun Luo* and Cory Brouwer *Correspondence: luo_weijun at yahoo.com Paper: http://bioinformatics.oxfordjournals.org/content/29/14/1830.full Bioconductor release: http://bioconductor.org/packages/release/bioc/html/pathview.html Pathview is a novel tool set that maps, integrates and renders a large variety of biological data on pathways, and produces interpretable graphs with publication quality. Pathview generates both native KEGG view and Graphviz view for pathways. KEGG view keeps all the pathway meta-data, including reaction and signaling contexts important for human reading and interpretation. Graphviz view provides better control of node and edge attributes, better view of pathway topology and analysis statistics. Pathview provides strong support for data integration. It works with: 1) essentially all types of biological data mappable to pathways, 2) over 10 types of gene or protein IDs, and 20 types of compound or metabolite IDs, 3) pathways for about 3000 species as well as KEGG Orthology, 4) various data attributes and formats, i.e. continuous/discrete data, matrices/vectors, single/multiple samples or time-series etc. Pathview is open source, fully automated and error-resistant. 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.