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>

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
Bioc Package Browser	https://code.bioconductor.org/browse/magrene/
Package Short Url	https://bioconductor.org/packages/magrene/
Package Downloads Report	Download Stats