DOI: 10.18129/B9.bioc.SBGNview  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see SBGNview.

"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

Bioconductor version: 3.17

SBGNview is a tool set for pathway based data visalization, integration and analysis. SBGNview is similar and complementary to the widely used Pathview, with the following key features: 1. Pathway definition by the widely adopted Systems Biology Graphical Notation (SBGN); 2. Supports multiple major pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP) and user defined pathways; 3. Covers 5,200 reference pathways and over 3,000 species by default; 4. Extensive graphics controls, including glyph and edge attributes, graph layout and sub-pathway highlight; 5. SBGN pathway data manipulation, processing, extraction and analysis.

Author: Xiaoxi Dong*, Kovidh Vegesna*, Weijun Luo

Maintainer: Weijun Luo <luo_weijun at>

Citation (from within R, enter citation("SBGNview")):


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HTML R Script Pathway analysis using SBGNview gene set
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biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, GeneTarget, Genetics, GraphAndNetwork, Metabolomics, Microarray, Pathways, Proteomics, RNASeq, Sequencing, Software, SystemsBiology, Visualization
Version 1.14.0
In Bioconductor since BioC 3.10 (R-3.6) (4 years)
License AGPL-3
Depends R (>= 3.6), pathview,
Imports Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph, rmarkdown, knitr, SummarizedExperiment, AnnotationDbi, httr, KEGGREST, bookdown
Suggests testthat, gage
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