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Showing content from https://www.bioconductor.org/packages/devel/bioc/html/../../bioc/html/../../bioc/html/gatom.html below:

Bioconductor - gatom (development version)

gatom

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 (3.22)

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 gmail.com>

Citation (from within R, enter citation("gatom")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("gatom")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("gatom")
Details biocViews DifferentialExpression, GeneExpression, Network, Pathways, Software Version 1.7.0 In Bioconductor since BioC 3.18 (R-4.3) (1.5 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) System Requirements URL https://github.com/ctlab/gatom/ Bug Reports https://github.com/ctlab/gatom/issues See More Suggests testthat, knitr, rmarkdown, KEGGREST, AnnotationDbi, org.Mm.eg.db, reactome.db, fgsea, readr, BiocStyle, R.utils Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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