gatom
This is thereleased version of gatom; for the devel version, seegatom.
Finding an Active Metabolic Module in Atom Transition Network
Bioconductor version: Release (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("gatom")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("gatom")For older versions of R, please refer to the appropriateBioconductor 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 | 1.8.4 |
| In Bioconductor since | BioC 3.18 (R-4.3) (2 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,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
FollowInstallation instructions to use this package in your R session.
| Source Package | gatom_1.8.4.tar.gz |
| Windows Binary (x86_64) | gatom_1.8.2.zip |
| macOS Binary (x86_64) | gatom_1.8.4.tgz |
| macOS Binary (arm64) | gatom_1.8.4.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 |
| Old Source Packages for BioC 3.22 | Source Archive |