Package: gatom 1.3.0

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]

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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'))

The latest version of this package failed to build. Look at thebuild logs for more information.

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-1.3.0(bioc 3.20)gatom-1.2.0(bioc 3.19)

bioconductor-package

15 exports 1.31 score 118 dependencies

Last updated 2 months agofrom:886bc8055c

Exports:abbreviateLabels addHighlyExpressedEdges collapseAtomsIntoMetabolites connectAtomsInsideMetabolite createShinyCyJSWidget getGeneDEMeta getMetDEMeta makeMetabolicGraph makeOrgGatomAnnotation prepareDE saveModuleToDot saveModuleToHtml saveModuleToPdf saveModuleToXgmml scoreGraph

Dependencies:AnnotationDbi askpass backports base64enc BH Biobase BiocGenerics BioNet Biostrings bit bit64 blob broom broom.helpers bslib cachem cli clipr coda codetools colorspace cpp11 crayon curl data.table DBI digest dplyr evaluate fansi farver fastmap fontawesome forcats fs generics GenomeInfoDb GenomeInfoDbData GGally ggplot2 ggstats glue graph gtable haven highr hms htmltools htmlwidgets httr igraph intergraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling labelled lattice lifecycle lobstr magrittr MASS Matrix memoise mgcv mime munsell mwcsr network nlme openssl patchwork pillar pkgconfig plogr plyr png prettyunits progress pryr purrr R6 rappdirs RBGL RColorBrewer Rcpp readr rlang rmarkdown RSQLite S4Vectors sass scales shinyCyJS sna statnet.common stringi stringr sys tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 vctrs viridisLite vroom withr xfun XML XVector yaml zlibbioc

Using gatom package

Anstasiia Gainullina, Mariia Emelianova, Alexey Sergushichev

Rendered fromgatom-tutorial.Rmdusingknitr::rmarkdownon May 31 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Abbreviate lipid labels for lipid module	abbreviateLabels
Add reactions without highly changing genes but with high average expression	addHighlyExpressedEdges
Collapse atoms belonging to the same metabolite into one vertex	collapseAtomsIntoMetabolites
Connect atoms belonging to the same metabolite with edges	connectAtomsInsideMetabolite
Creates shinyCyJS widget from module	createShinyCyJSWidget
gatom: a package for finding an active metabolic module in atom transition network	gatom
Example gene differential expression data.	gene.de.rawEx
Finds columns in gene differential expression table required for gatom analysis	getGeneDEMeta
Generate list of metabolic pathways from Reactome and KEGG databases	getMetabolicPathways
Finds columns in differential expression table for metabolites required for gatom analysis	getMetDEMeta
Example metabolic graph with atom topology.	gEx
Example scored metabolic graph with atom topology.	gsEx
Creates metabolic graph based on specified data	makeMetabolicGraph
Create an organism annotation object for network analysis	makeOrgGatomAnnotation
Example metabolite differential abundance data.	met.de.rawEx
Example KEGG-based metabolite database object	met.kegg.dbEx
Example metabolic module.	mEx
Example KEGG-based network object	networkEx
Example organism annotation object	org.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 object	prepareDE
Save module to a graphviz dot file	saveModuleToDot
Save module to a html widget	saveModuleToHtml
Save module to a nice pdf file	saveModuleToPdf
Save module to an XGMML file	saveModuleToXgmml
Score metabolic graph	scoreGraph