[BioC] ISMB talks: Pathview for pathway-based data integration and visualization

Luo Weijun luo_weijun at yahoo.com
Fri Jul 11 17:09:49 CEST 2014


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.



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