SBGNview

DOI: 10.18129/B9.bioc.SBGNview    

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

Bioconductor version: Release (3.13)

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 "4.1") and enter:

if (!requireNamespace("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 1.6.0
In Bioconductor since BioC 3.10 (R-3.6) (1.5 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
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_1.6.0.tar.gz
Windows Binary SBGNview_1.6.0.zip
macOS 10.13 (High Sierra) SBGNview_1.6.0.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

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