MOGAMUN
This is the development version of MOGAMUN; for the stable release version, see MOGAMUN.
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks
Bioconductor version: Development (3.24)
MOGAMUN is a multi-objective genetic algorithm that identifies active modules in a multiplex biological network. This allows analyzing different biological networks at the same time. MOGAMUN is based on NSGA-II (Non-Dominated Sorting Genetic Algorithm, version II), which we adapted to work on networks.
Author: Elva-María Novoa-del-Toro [aut, cre]
Maintainer: Elva-María Novoa-del-Toro <elvanov at hotmail.com>
citation("MOGAMUN")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("MOGAMUN")
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("MOGAMUN")| Finding active modules with MOGAMUN | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiomedicalInformatics, Clustering, DifferentialExpression, GraphAndNetwork, Network, Software, SystemsBiology, Transcriptomics |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | GPL-3 + file LICENSE |
| Depends | |
| Imports | stats, utils, RCy3, stringr, graphics, grDevices, RUnit, BiocParallel, igraph |
| System Requirements | |
| URL | https://github.com/elvanov/MOGAMUN |
See More
| Suggests | knitr, markdown |
| 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 | MOGAMUN_1.23.0.tar.gz |
| Windows Binary (x86_64) | MOGAMUN_1.23.0.zip |
| macOS Binary (big-sur-x86_64) | MOGAMUN_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | MOGAMUN_1.23.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MOGAMUN |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MOGAMUN |
| Bioc Package Browser | https://code.bioconductor.org/browse/MOGAMUN/ |
| Package Short Url | https://bioconductor.org/packages/MOGAMUN/ |
| Package Downloads Report | Download Stats |