News:SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
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Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 2 days ago
United States

Dear all,
The new SBGNview package has been released with major updates and improvement:
GitHub
https://github.com/datapplab/SBGNview
BioC
https://bioconductor.org/packages/SBGNview/

SBGNview is a tool set for pathway based data visualization, integration and analysis. SBGNview is similar and complementary to the widely used Pathview package, with the following key features:
• Pathway definition by the widely adopted Systems Biology Graphical Notation (SBGN);
• Supports multiple major pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP etc) and user defined pathways;
• Covers 5,200 reference pathways and over 3,000 species by default;
• Extensive graphics controls, including glyph and edge attributes, graph layout and sub-pathway highlight;
• SBGN pathway data manipulation, processing, extraction and analysis.

You may find an overview and quick start examples here:
https://github.com/datapplab/SBGNview
Main tutorial:
https://bioconductor.org/packages/release/bioc/vignettes/SBGNview/inst/doc/SBGNview.Vignette.html
Analysis workflow:
https://bioconductor.org/packages/release/bioc/vignettes/SBGNview/inst/doc/pathway.enrichment.analysis.html

Please try it out and let us know if you have any comments/suggestions. Thank you!

SBGNview pathways SBGNview.data pathview visualization • 155 views
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Entering edit mode
Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 2 days ago
United States

To install and use the latest updates of SBGNview via BioC, i.e.

BiocManager::install("SBGNview")

users may need to first update to the current Bioconductor release version 3.12 or devel version 3.13.

Note SBGNview works with major pathway databases other than KEGG
pathview focuses on KEGG
https://bioconductor.org/packages/pathview/

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