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 (3.24)
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("gatom")):
Installation
To install this package, start R (version "4.6") 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")| Using gatom package | HTML | R Script |
| Reference Manual |
Details
| biocViews | DifferentialExpression, GeneExpression, Network, Pathways, Software |
| Version | 1.11.4 |
| In Bioconductor since | BioC 3.18 (R-4.3) (2.5 years) |
| License | MIT + file LICENCE |
| Depends | R (>= 4.3.0) |
| Imports | data.table, igraph, BioNet, plyr, methods, XML, sna, intergraph, network, ggnetwork, scales, grid, ggplot2, mwcsr, 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(>= 1.53.2), 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.
| Source Package | gatom_1.11.4.tar.gz |
| Windows Binary (x86_64) | gatom_1.11.4.zip |
| macOS Binary (big-sur-x86_64) | gatom_1.11.4.tgz |
| macOS Binary (sonoma-arm64) | gatom_1.11.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/gatom |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/gatom |
| Bioc Package Browser | https://code.bioconductor.org/browse/gatom/ |
| Package Short Url | https://bioconductor.org/packages/gatom/ |
| Package Downloads Report | Download Stats |