SBGNview

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SBGNview.

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

Bioconductor version: 3.12

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 yahoo.com>

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

Installation

To install this package, start R (version "4.0") 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
Quick start SBGNview	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	1.4.1
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, httr, KEGGREST, bookdown
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_1.4.1.tar.gz
Windows Binary	SBGNview_1.4.1.zip
macOS 10.13 (High Sierra)	SBGNview_1.4.1.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 3.12	Source Archive