Package: gatom 1.11.0

Alexey Sergushichev

gatom: Finding an Active Metabolic Module in Atom Transition Network

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.

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

gatom_1.11.0.tar.gz
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gatom_1.11.0.tgz(r-4.6-any)gatom_1.11.0.tgz(r-4.5-any)
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gatom_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
gatom/json (API)

# Install 'gatom' in R:
install.packages('gatom', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ctlab/gatom/issues

Datasets:
  • gene.de.rawEx - Example gene differential expression data.
  • gEx - Example metabolic graph with atom topology.
  • gsEx - Example scored metabolic graph with atom topology.
  • met.de.rawEx - Example metabolite differential abundance data.
  • met.kegg.dbEx - Example KEGG-based metabolite database object
  • mEx - Example metabolic module.
  • networkEx - Example KEGG-based network object
  • org.Mm.eg.gatom.annoEx - Example organism annotation object

On BioConductor:gatom-1.11.0(bioc 3.24)gatom-1.10.0(bioc 3.23)

geneexpressiondifferentialexpressionpathwaysnetwork

5.80 score 8 stars 13 scripts 312 downloads 15 exports 86 dependencies

Last updated from:736ab92b6c. Checks:8 NOTE, 2 OK. Indexed: yes.

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source / vignettesOK490
linux-release-x86_64NOTE484
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Exports:abbreviateLabelsaddHighlyExpressedEdgescollapseAtomsIntoMetabolitesconnectAtomsInsideMetabolitecreateShinyCyJSWidgetgetGeneDEMetagetMetDEMetamakeMetabolicGraphmakeOrgGatomAnnotationprepareDEsaveModuleToDotsaveModuleToHtmlsaveModuleToPdfsaveModuleToXgmmlscoreGraph

Dependencies:AnnotationDbiaskpassbase64encBHBiobaseBiocGenericsBioNetBiostringsbitbit64blobbslibcachemclicodacpp11crayoncurldata.tableDBIdigestevaluatefarverfastmapfontawesomefsgenericsggnetworkggplot2ggrepelgluegraphgtablehighrhtmltoolshtmlwidgetshttrigraphintergraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglatticelifecyclemagrittrMatrixmemoisemimemwcsrnetworkopensslpillarpkgconfigplyrpngR6rappdirsRBGLRColorBrewerRcpprlangrmarkdownRSQLiteS4VectorsS7sassscalesSeqinfoshinyCyJSsnastatnet.commonsystibbletinytexutf8vctrsviridisLitewithrxfunXMLXVectoryaml

Using gatom package

Anstasiia Gainullina, Mariia Emelianova, Alexey Sergushichev

Rendered fromgatom-tutorial.Rmdusingknitr::rmarkdownon May 14 2026.

Last update: 2023-10-15
Started: 2018-03-09

Readme and manuals

Help Manual

Help pageTopics
Abbreviate lipid labels for lipid moduleabbreviateLabels
Add reactions without highly changing genes but with high average expressionaddHighlyExpressedEdges
Collapse atoms belonging to the same metabolite into one vertexcollapseAtomsIntoMetabolites
Connect atoms belonging to the same metabolite with edgesconnectAtomsInsideMetabolite
Creates shinyCyJS widget from modulecreateShinyCyJSWidget
Example gene differential expression data.gene.de.rawEx
Finds columns in gene differential expression table required for gatom analysisgetGeneDEMeta
Generate list of metabolic pathways from Reactome and KEGG databasesgetMetabolicPathways
Finds columns in differential expression table for metabolites required for gatom analysisgetMetDEMeta
Example metabolic graph with atom topology.gEx
Example scored metabolic graph with atom topology.gsEx
Creates metabolic graph based on specified datamakeMetabolicGraph
Create an organism annotation object for network analysismakeOrgGatomAnnotation
Example metabolite differential abundance data.met.de.rawEx
Example KEGG-based metabolite database objectmet.kegg.dbEx
Example metabolic module.mEx
Example KEGG-based network objectnetworkEx
Example organism annotation objectorg.Mm.eg.gatom.annoEx
Makes data.table with differential expression results containing all columns required for gatom and in the expected format based on metadata objectprepareDE
Save module to a graphviz dot filesaveModuleToDot
Save module to a html widgetsaveModuleToHtml
Save module to a nice pdf filesaveModuleToPdf
Save module to an XGMML filesaveModuleToXgmml
Score metabolic graphscoreGraph