SBGNview
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
Bioconductor version: 3.24 · Package version: 1.27.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SBGNview")Details
| Maintainer | Weijun Luo <luo_weijun@yahoo.com> |
| Author | Xiaoxi Dong*, Kovidh Vegesna*, Weijun Luo |
| License | AGPL-3 |
| URL | https://github.com/datapplab/SBGNview |
| Bug Reports | https://github.com/datapplab/SBGNview/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, GeneTarget, Genetics, GraphAndNetwork, Metabolomics, Microarray, Pathways, Proteomics, RNASeq, Sequencing, Software, SystemsBiology, Visualization |
| Package Short Url | https://bioconductor.org/packages/SBGNview/ |
Citation
From within R, enter 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 1.27.0, https://bioconductor.org/packages/SBGNview.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- SBGNview Based Pathway Analysis and Visualization Workflow
- SBGNview Quick Start
- SBGNview: Data Analysis, Integration and Visualization on Massive SBGN Pathway Collections
Download
Follow the installation instructions to use this package in your R session.
| Source package | SBGNview_1.27.0.tar.gz |
| Windows binary (x86_64) | SBGNview_1.27.0.zip |
| macOS binary (arm64) | SBGNview_1.27.0.tgz |
| macOS binary (x86_64) | SBGNview_1.27.0.tgz |
Dependencies
Depends: R (>= 3.6), pathview, SBGNview.data
Imports: Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph, rmarkdown, knitr, SummarizedExperiment, AnnotationDbi, httr, KEGGREST, bookdown