magrene
This is thereleased version of magrene; for the devel version, seemagrene.
Motif Analysis In Gene Regulatory Networks
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0002-5314-2964, Yves Van de Peer [aut] ORCID: 0000-0003-4327-3730
Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva at hotmail.com>
citation("magrene")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("magrene")For older versions of R, please refer to the appropriateBioconductor 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 | 1.12.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (3 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
FollowInstallation instructions to use this package in your R session.
| Source Package | magrene_1.12.0.tar.gz |
| Windows Binary (x86_64) | magrene_1.12.0.zip (64-bit only) |
| macOS Binary (x86_64) | magrene_1.12.0.tgz |
| macOS Binary (arm64) | magrene_1.12.0.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 |