gatom
Finding an Active Metabolic Module in Atom Transition Network
Bioconductor version: 3.23 · Package version: 1.10.2
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module) most regulated between the two conditions of interest. The package further provides functions for module post-processing, annotation and visualization.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("gatom")Details
| Maintainer | Alexey Sergushichev <alsergbox@gmail.com> |
| Author | Anastasiia Gainullina [aut], Mariia Emelianova [aut], Alexey Sergushichev [aut, cre] |
| License | MIT + file LICENCE |
| URL | https://github.com/ctlab/gatom/ |
| Bug Reports | https://github.com/ctlab/gatom/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, Network, Pathways, Software |
| Package Short Url | https://bioconductor.org/packages/gatom/ |
Citation
From within R, enter citation("gatom"):
Anastasiia Gainullina, Mariia Emelianova, Alexey Sergushichev. gatom: Finding an Active Metabolic Module in Atom Transition Network. doi:10.18129/B9.bioc.gatom, R package version 1.10.2, https://bioconductor.org/packages/gatom.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | gatom_1.10.2.tar.gz |
| Windows binary (x86_64) | gatom_1.10.2.zip |
| macOS binary (arm64) | gatom_1.10.2.tgz |
| macOS binary (x86_64) | gatom_1.10.2.tgz |
Dependencies
Depends: R (>= 4.3.0)
Imports: data.table, igraph, BioNet, plyr, methods, XML, sna, intergraph, network, ggnetwork, scales, grid, ggplot2, mwcsr, htmlwidgets, htmltools, shinyCyJS (>= 1.0.0)
Suggests: testthat, knitr, rmarkdown, KEGGREST (>= 1.52.2), AnnotationDbi, org.Mm.eg.db, reactome.db, fgsea, readr, BiocStyle, R.utils