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!