magrene
This is the development version of magrene; for the stable release version, see magrene.
Motif Analysis In Gene Regulatory Networks
Bioconductor version: Development (3.24)
magrene allows the identification and analysis of graph motifs in (duplicated) gene regulatory networks (GRNs), including lambda, V, PPI V, delta, and bifan motifs. GRNs can be tested for motif enrichment by comparing motif frequencies to a null distribution generated from degree-preserving simulated GRNs. Motif frequencies can be analyzed in the context of gene duplications to explore the impact of small-scale and whole-genome duplications on gene regulatory networks. Finally, users can calculate interaction similarity for gene pairs based on the Sorensen-Dice similarity index.
Author: Fabrício Almeida-Silva [aut, cre]
, Yves Van de Peer [aut]
Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva at hotmail.com>
citation("magrene")):
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("magrene")
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("magrene")| Introduction to magrene | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GraphAndNetwork, MotifDiscovery, NetworkEnrichment, Software, SystemsBiology |
| Version | 1.15.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 years) |
| License | GPL-3 |
| Depends | R (>= 4.2.0) |
| Imports | utils, stats, BiocParallel |
| System Requirements | |
| URL | https://github.com/almeidasilvaf/magrene |
| Bug Reports | https://support.bioconductor.org/t/magrene |
See More
| Suggests | BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo, testthat (>= 3.0.0) |
| 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 | magrene_1.15.0.tar.gz |
| Windows Binary (x86_64) | magrene_1.15.0.zip |
| macOS Binary (big-sur-x86_64) | magrene_1.15.0.tgz |
| macOS Binary (sonoma-arm64) | magrene_1.15.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/magrene |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/magrene |
| Bioc Package Browser | https://code.bioconductor.org/browse/magrene/ |
| Package Short Url | https://bioconductor.org/packages/magrene/ |
| Package Downloads Report | Download Stats |