gatom
This is the released version of gatom; for the devel version, see gatom.
Finding an Active Metabolic Module in Atom Transition Network
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.10.2 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 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(>= 1.52.2), 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_1.10.2.tar.gz |
| Windows Binary (x86_64) | gatom_1.10.2.zip |
| macOS Binary (big-sur-x86_64) | gatom_1.10.2.tgz |
| macOS Binary (sonoma-arm64) | gatom_1.10.2.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 3.23 | Source Archive |