datapplab/SBGNview: Overlay omics data onto SBGN pathway diagram

SBGNview is a tool set for visualizing omics data on pathway maps and pathway related data analysis. Given an omics data table and a pathway file (SBGN-ML format with layout information), SBGNview overlays omics data as colors on glyphs (nodes) and output image files. Pathway is rendered with community standard notation: Systems Biology Graphical Notation (SBGN). Currently it maps gene/protein data to “macromolecule” glyphs and maps chemical compound data to “simple chemical” glyphs. For omics data, SBGNview supports common gene/protein/compound ID types (e.g. Entrez Gene ID, UNIPROT, ChEBI etc.). SBGNview can automatically retrieve and use SBGN-ML files from common pathway databases (e.g. Reactome, MetaCyc, SMPDB, PANTHER, METACROP etc.). Extensive options are provided to control glyph and edge features. SBGNview can search for pathways by keywords, extract node information and highlight shortest path between two nodes.

Getting started

Package details

Author Xiaoxi Dong, Weijun Luo
Bioconductor views DifferentialExpression GeneExpression GeneSetEnrichment GeneTarget Genetics GraphAndNetwork Metabolomics Microarray Pathways Proteomics RNASeq Sequencing SystemsBiology Visualization
MaintainerXiaoxi Dong <[email protected]>
LicenseAGPL-3
Version0.99.37
URL https://github.com/datapplab/SBGNview
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("datapplab/SBGNview")
datapplab/SBGNview documentation built on July 3, 2019, 5:21 a.m.