SBGNview

DOI: 10.18129/B9.bioc.SBGNview    

Overlay omics data onto SBGN pathway diagram

Bioconductor version: Release (3.11)

SBGNview is an R package for visualizing omics data on SBGN pathway maps. Given omics data and a SBGN-ML file with layout information, SBGNview can display omics data as colors on glyphs and output image files. SBGNview provides extensive options to control glyph and edge features (e.g. color, line width etc.). To facilitate pathway based analysis, SBGNview also provides functions to extract molecule sets from SBGN-ML files. SBGNview can map a large collection of gene, protein and compound ID typs to glyphs.

Author: Xiaoxi Dong, Weijun Luo

Maintainer: Xiaoxi Dong <dfdongxiaoxi at gmail.com>

Installation

To install this package, start R (version "4.0") 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	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	1.2.0
In Bioconductor since	BioC 3.10 (R-3.6) (1 year)
License	AGPL-3
Depends	R (>= 3.6), pathview, SBGNview.data
Imports	Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph, rmarkdown, knitr, SummarizedExperiment, AnnotationDbi
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_1.2.0.tar.gz
Windows Binary	SBGNview_1.2.0.zip
macOS 10.13 (High Sierra)	SBGNview_1.2.0.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
Old Source Packages for BioC 3.11	Source Archive