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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SBGNview")

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

Documentation

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

browseVignettes("SBGNview")

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

Need some help? Ask on the Bioconductor Support site!

Details

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) (4.5 years)
License	AGPL-3
Depends	R (>= 3.6), pathview, SBGNview.data
Imports	Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph, rmarkdown, knitr, SummarizedExperiment, AnnotationDbi
System Requirements
URL	https://github.com/datapplab/SBGNview
Bug Reports	https://github.com/datapplab/SBGNview/issues

Suggests	testthat, gage
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	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	SBGNview_1.0.0.zip
Mac OS X 10.11 (El Capitan)	SBGNview_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SBGNview
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SBGNview
Bioc Package Browser	https://code.bioconductor.org/browse/SBGNview/
Package Short Url	https://bioconductor.org/packages/SBGNview/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.10	Source Archive