SBGNview
This is the released version of SBGNview; for the devel version, see SBGNview.
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
Bioconductor version: Release (3.23)
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")):Xiaoxi Dong*, Kovidh Vegesna*, Weijun Luo. SBGNview: "SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways". doi:10.18129/B9.bioc.SBGNview, R package version 1.26.0, https://bioconductor.org/packages/SBGNview.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 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, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SBGNview_1.26.0.tar.gz |
| Windows Binary (x86_64) | SBGNview_1.26.0.zip |
| macOS Binary (big-sur-x86_64) | SBGNview_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | SBGNview_1.26.0.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 |