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

TitlePathview: an R/Bioconductor package for pathway-based data integration and visualization.
Publication TypeJournal Article
Year of Publication2013
AuthorsLuo W, Brouwer C
JournalBioinformatics
Volume29
Issue14
Pagination1830-1
Date Published2013 Jul 15
ISSN1367-4811
KeywordsComputer Graphics, Gene Expression, Metabolic Networks and Pathways, Signal Transduction, Software, Systems Integration
Abstract

<p><b>SUMMARY: </b>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.</p><p><b>AVAILABILITY: </b>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/.</p><p><b>CONTACT: </b>luo_weijun@yahoo.com</p><p><b>SUPPLEMENTARY INFORMATION: </b>Supplementary data are available at Bioinformatics online.</p>

DOI10.1093/bioinformatics/btt285
Alternate JournalBioinformatics
PubMed ID23740750
PubMed Central IDPMC3702256