SBGNview

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see SBGNview.

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

Bioconductor version: 3.21

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 "4.5") 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 1.22.0

In Bioconductor since BioC 3.10 (R-3.6) (6 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

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Package Archives

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

Source Package SBGNview_1.22.0.tar.gz

Windows Binary (x86_64) SBGNview_1.22.0.zip

macOS Binary (x86_64) SBGNview_1.22.0.tgz

macOS Binary (arm64) SBGNview_1.22.0.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/

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