SBGNview
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
Bioconductor version: Release (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("SBGNview")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text |
Details
biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, GeneTarget, Genetics, GraphAndNetwork, Metabolomics, Microarray, Pathways, Proteomics, RNASeq, Sequencing, Software, SystemsBiology, Visualization |
Version | 1.20.0 |
In Bioconductor since | BioC 3.10 (R-3.6) (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 |
See More
Suggests | testthat, gage |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | SBGNview_1.20.0.tar.gz |
Windows Binary (x86_64) | SBGNview_1.20.0.zip |
macOS Binary (x86_64) | SBGNview_1.20.0.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 |