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This is the development version of gatom; for the stable release version, see gatom.

Finding an Active Metabolic Module in Atom Transition Network

Bioconductor version: Development (3.20)

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>

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biocViews DifferentialExpression, GeneExpression, Network, Pathways, Software
Version 1.3.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)
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)
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Suggests testthat, knitr, rmarkdown, KEGGREST, AnnotationDbi,, reactome.db, fgsea, readr, BiocStyle, R.utils
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