SBGNview

DOI: 10.18129/B9.bioc.SBGNview    

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

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, GeneTarget, Genetics, GraphAndNetwork, Metabolomics, Microarray, Pathways, Proteomics, RNASeq, Sequencing, Software, SystemsBiology, Visualization
Version	1.10.0
In Bioconductor since	BioC 3.10 (R-3.6) (3 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
LinkingTo
Suggests	testthat, gage
SystemRequirements
Enhances
URL	https://github.com/datapplab/SBGNview
BugReports	https://github.com/datapplab/SBGNview/issues
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_1.10.0.tar.gz
Windows Binary	SBGNview_1.10.0.zip
macOS Binary (x86_64)	SBGNview_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SBGNview
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SBGNview
Package Short Url	https://bioconductor.org/packages/SBGNview/
Package Downloads Report	Download Stats