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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/SBGNview/ |
| Package Short Url | https://bioconductor.org/packages/SBGNview/ |
| Package Downloads Report | Download Stats |