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SBGNview

This is the development version of SBGNview; for the stable release version, see SBGNview.

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


Bioconductor version: Development (3.20)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, GeneTarget, Genetics, GraphAndNetwork, Metabolomics, Microarray, Pathways, Proteomics, RNASeq, Sequencing, Software, SystemsBiology, Visualization
Version 1.19.0
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, httr, KEGGREST, bookdown
System Requirements
URL https://github.com/datapplab/SBGNview
Bug Reports https://github.com/datapplab/SBGNview/issues
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Suggests testthat, gage
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Package Archives

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

Source Package SBGNview_1.19.0.tar.gz
Windows Binary SBGNview_1.19.0.zip (64-bit only)
macOS Binary (x86_64) SBGNview_1.19.0.tgz
macOS Binary (arm64) SBGNview_1.19.0.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