Package: gatom 1.11.4

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_1.11.4.tar.gz
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gatom_1.11.4.tgz(r-4.6-any)gatom_1.11.4.tgz(r-4.5-any)
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gatom_1.11.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
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)

geneexpression differentialexpression pathways network

5.98 score 8 stars 16 scripts 15 exports 86 dependencies

Last updated from:4bd914ef0a. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	251
linux-devel-x86_64	NOTE	420
source / vignettes	OK	501
linux-release-x86_64	NOTE	401
macos-release-arm64	NOTE	223
macos-oldrel-arm64	NOTE	303
windows-devel	NOTE	314
windows-release	NOTE	303
windows-oldrel	NOTE	297
wasm-release	OK	238

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

Dependencies:AnnotationDbi askpass base64enc BH Biobase BiocGenerics BioNet Biostrings bit bit64 blob bslib cachem cli coda cpp11 crayon curl data.table DBI digest evaluate farver fastmap fontawesome fs generics ggnetwork ggplot2 ggrepel glue graph gtable highr htmltools htmlwidgets httr igraph intergraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lattice lifecycle magrittr Matrix memoise mime mwcsr network openssl pillar pkgconfig plyr png R6 rappdirs RBGL RColorBrewer Rcpp rlang rmarkdown RSQLite S4Vectors S7 sass scales Seqinfo shinyCyJS sna statnet.common sys tibble tinytex utf8 vctrs viridisLite withr xfun XML XVector yaml

Using gatom package

Rendered fromgatom-tutorial.Rmdusingknitr::rmarkdown

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
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