MetaboSignal
This is the released version of MetaboSignal; for the devel version, see MetaboSignal.
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
Bioconductor version: Release (3.23)
MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.
Author: Andrea Rodriguez-Martinez, Rafael Ayala, Joram M. Posma, Ana L. Neves, Maryam Anwar, Jeremy K. Nicholson, Marc-Emmanuel Dumas
Maintainer: Andrea Rodriguez-Martinez <andrea.rodriguez-martinez13 at imperial.ac.uk>, Rafael Ayala <rafaelayalahernandez at gmail.com>
citation("MetaboSignal")):
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("MetaboSignal")
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("MetaboSignal")| MetaboSignal | HTML | R Script |
| MetaboSignal 2: merging KEGG with additional interaction resources | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneSignaling, GeneTarget, GraphAndNetwork, KEGG, Network, Pathways, Reactome, Software |
| Version | 1.42.1 |
| In Bioconductor since | BioC 3.4 (R-3.3) (10 years) |
| License | GPL-3 |
| Depends | R (>= 3.3) |
| Imports | KEGGgraph, hpar, igraph, RCurl, KEGGREST, EnsDb.Hsapiens.v75, stats, graphics, utils, org.Hs.eg.db, biomaRt, AnnotationDbi, MWASTools, mygene |
| System Requirements | |
| URL |
See More
| Suggests | RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown |
| 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 | MetaboSignal_1.42.1.tar.gz |
| Windows Binary (x86_64) | MetaboSignal_1.42.1.zip |
| macOS Binary (big-sur-x86_64) | MetaboSignal_1.42.1.tgz |
| macOS Binary (sonoma-arm64) | MetaboSignal_1.42.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MetaboSignal |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MetaboSignal |
| Bioc Package Browser | https://code.bioconductor.org/browse/MetaboSignal/ |
| Package Short Url | https://bioconductor.org/packages/MetaboSignal/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |