SBGNview

DOI: 10.18129/B9.bioc.SBGNview    

This is the development version of SBGNview; to use it, please install the devel version of Bioconductor.

Overlay omics data onto SBGN pathway diagram

Bioconductor version: Development (3.10)

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>

Citation (from within R, enter citation("SBGNview")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

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 0.99.37
In Bioconductor since BioC 3.10 (R-3.6)
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_0.99.37.tar.gz
Windows Binary SBGNview_0.99.37.zip
Mac OS X 10.11 (El Capitan) SBGNview_0.99.37.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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