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gatom

Finding an Active Metabolic Module in Atom Transition Network


Bioconductor version: Release (3.18)

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.

Author: Anastasiia Gainullina [aut], Mariia Emelianova [aut], Alexey Sergushichev [aut, cre]

Maintainer: Alexey Sergushichev <alsergbox at gmail.com>

Citation (from within R, enter citation("gatom")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("gatom")

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("gatom")
Using gatom package HTML R Script
Reference Manual PDF

Details

biocViews DifferentialExpression, GeneExpression, Network, Pathways, Software
Version 1.0.0
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License MIT + file LICENCE
Depends R (>= 4.3.0)
Imports data.table, igraph, BioNet, plyr, methods, XML, sna, intergraph, network, GGally, grid, ggplot2, mwcsr, pryr, htmlwidgets, htmltools, shinyCyJS (>= 1.0.0)
System Requirements
URL https://github.com/ctlab/gatom/
Bug Reports https://github.com/ctlab/gatom/issues
See More
Suggests testthat, knitr, rmarkdown, KEGGREST, AnnotationDbi, org.Mm.eg.db, reactome.db, fgsea, readr, BiocStyle, R.utils
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package gatom_1.0.0.tar.gz
Windows Binary gatom_1.0.0.zip
macOS Binary (x86_64) gatom_1.0.0.tgz
macOS Binary (arm64) gatom_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/gatom
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/gatom
Bioc Package Browser https://code.bioconductor.org/browse/gatom/
Package Short Url https://bioconductor.org/packages/gatom/
Package Downloads Report Download Stats