SBGNview
This is thereleased version of SBGNview; for the devel version, seeSBGNview.
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
Bioconductor version: Release (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("SBGNview")For older versions of R, please refer to the appropriateBioconductor 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 | 1.24.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (6 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
FollowInstallation instructions to use this package in your R session.
| Source Package | SBGNview_1.24.0.tar.gz |
| Windows Binary (x86_64) | SBGNview_1.24.0.zip |
| macOS Binary (x86_64) | SBGNview_1.24.0.tgz |
| macOS Binary (arm64) | SBGNview_1.24.0.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 |