DOI: 10.18129/B9.bioc.SBGNview    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see SBGNview.

Overlay omics data onto SBGN pathway diagram

Bioconductor version: 3.10

SBGNview is an R package for visualizing omics data on SBGN pathway maps. Given omics data and a SBGN-ML file with layout information, SBGNview can display omics data as colors on glyphs and output image files. SBGNview provides extensive options to control glyph and edge features (e.g. color, line width etc.). To facilitate pathway based analysis, SBGNview also provides functions to extract molecule sets from SBGN-ML files. SBGNview can map a large collection of gene, protein and compound ID typs to glyphs.

Author: Xiaoxi Dong, Weijun Luo

Maintainer: Xiaoxi Dong <dfdongxiaoxi at>

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


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script Pathway analysis using SBGNview gene set
HTML R Script SBGNview functions
PDF   Reference Manual
Text   NEWS


biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, GeneTarget, Genetics, GraphAndNetwork, Metabolomics, Microarray, Pathways, Proteomics, RNASeq, Sequencing, Software, SystemsBiology, Visualization
Version 1.0.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
License AGPL-3
Depends R (>= 3.6), pathview,
Imports Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph, rmarkdown, knitr, SummarizedExperiment, AnnotationDbi
Suggests testthat, gage
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SBGNview_1.0.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) SBGNview_1.0.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: