gatom

DOI: 10.18129/B9.bioc.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>

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")

 

HTML	R Script	Using gatom package
PDF		Reference Manual

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)
LinkingTo
Suggests	testthat, knitr, rmarkdown, KEGGREST, AnnotationDbi, org.Mm.eg.db, reactome.db, fgsea, readr, BiocStyle, R.utils
SystemRequirements
Enhances
URL	https://github.com/ctlab/gatom/
BugReports	https://github.com/ctlab/gatom/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

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
Old Source Packages for BioC 3.18	Source Archive