magrene

DOI: 10.18129/B9.bioc.magrene    

Motif Analysis In Gene Regulatory Networks

Bioconductor version: Release (3.16)

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 "4.2") 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")

 

HTML R Script Introduction to magrene
PDF   Reference Manual
Text   NEWS

Details

biocViews GraphAndNetwork, MotifDiscovery, NetworkEnrichment, Software, SystemsBiology
Version 1.0.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
License GPL-3
Depends R (>= 4.2.0)
Imports utils, stats, BiocParallel
LinkingTo
Suggests BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL https://github.com/almeidasilvaf/magrene
BugReports https://support.bioconductor.org/t/magrene
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package magrene_1.0.0.tar.gz
Windows Binary magrene_1.0.0.zip
macOS Binary (x86_64) magrene_1.0.0.tgz
macOS Binary (arm64) magrene_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/magrene
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/magrene
Package Short Url https://bioconductor.org/packages/magrene/
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