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magrene

Motif Analysis In Gene Regulatory Networks


Bioconductor version: Release (3.18)

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 (from within R, enter citation("magrene")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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 PDF
NEWS Text

Details

biocViews GraphAndNetwork, MotifDiscovery, NetworkEnrichment, Software, SystemsBiology
Version 1.4.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 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)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package magrene_1.4.0.tar.gz
Windows Binary magrene_1.4.0.zip (64-bit only)
macOS Binary (x86_64) magrene_1.4.0.tgz
macOS Binary (arm64) magrene_1.4.0.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