Package: gatom 1.5.0

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_1.5.0.tar.gz
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gatom.pdf |gatom.html✨
gatom/json (API)

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

Peer review:

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

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

On BioConductor:gatom-1.5.0(bioc 3.21)gatom-1.4.0(bioc 3.20)

geneexpressiondifferentialexpressionpathwaysnetwork

5.18 score 5 stars 8 scripts 127 downloads 15 exports 109 dependencies

Last updated 2 months agofrom:97bd9cf0b3. Checks:OK: 1 NOTE: 5 ERROR: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 10 2024
R-4.5-winNOTEDec 10 2024
R-4.5-linuxNOTEDec 10 2024
R-4.4-winNOTEDec 10 2024
R-4.4-macERRORDec 10 2024
R-4.3-winNOTEDec 10 2024
R-4.3-macNOTEDec 10 2024

Exports:abbreviateLabelsaddHighlyExpressedEdgescollapseAtomsIntoMetabolitesconnectAtomsInsideMetabolitecreateShinyCyJSWidgetgetGeneDEMetagetMetDEMetamakeMetabolicGraphmakeOrgGatomAnnotationprepareDEsaveModuleToDotsaveModuleToHtmlsaveModuleToPdfsaveModuleToXgmmlscoreGraph

Dependencies:AnnotationDbiaskpassbase64encBHBiobaseBiocGenericsBioNetBiostringsbitbit64blobbslibcachemclicodacodetoolscolorspacecpp11crayoncurldata.tableDBIdigestdplyrevaluatefansifarverfastmapfontawesomeforcatsfsgenericsGenomeInfoDbGenomeInfoDbDataGGallyggplot2ggstatsgluegraphgtablehighrhmshtmltoolshtmlwidgetshttrigraphintergraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglatticelifecyclelobstrmagrittrMASSMatrixmemoisemgcvmimemunsellmwcsrnetworknlmeopensslpatchworkpillarpkgconfigplogrplyrpngprettyunitsprogresspryrpurrrR6rappdirsRBGLRColorBrewerRcpprlangrmarkdownRSQLiteS4VectorssassscalesshinyCyJSsnastatnet.commonstringistringrsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXMLXVectoryamlzlibbioc

Using gatom package

Anstasiia Gainullina, Mariia Emelianova, Alexey Sergushichev

Rendered fromgatom-tutorial.Rmdusingknitr::rmarkdownon Dec 10 2024.

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
gatom: a package for finding an active metabolic module in atom transition networkgatom
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