In almeidasilvaf/magrene: Motif Analysis In Gene Regulatory Networks

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)

magrene

The goal of magrene is to identify and analyze graph motifs containing duplicated genes in gene regulatory networks (GRNs). Possible motifs include V, PPI V, lambda, delta, and bifans.

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.

Additionally, GRNs can be tested for motif enrichment by comparing motif frequencies to a null distribution generated from degree-preserving simulated GRNs.

Finally, users can calculate the interaction similarity between gene pairs based on the Sorensen-Dice similarity index.

knitr::include_graphics("vignettes/motifs_vignette.png")

Installation instructions

Get the latest stable R release from CRAN. Then install magrene using from Bioconductor the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("magrene")

And the development version from GitHub with:

BiocManager::install("almeidasilvaf/magrene")

Citation

Below is the citation output from using citation('magrene') in R. Please run this yourself to check for any updates on how to cite magrene.

print(citation('magrene'), bibtex = TRUE)

Please note that magrene was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

Code of Conduct

Please note that the magrene project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Development tools

Continuous code testing is possible thanks to GitHub actions through r BiocStyle::CRANpkg('usethis'), r BiocStyle::CRANpkg('remotes'), and r BiocStyle::CRANpkg('rcmdcheck') customized to use Bioconductor's docker containers and r BiocStyle::Biocpkg('BiocCheck').
Code coverage assessment is possible thanks to codecov and r BiocStyle::CRANpkg('covr').
The documentation website is automatically updated thanks to r BiocStyle::CRANpkg('pkgdown').
The documentation is formatted thanks to r BiocStyle::CRANpkg('devtools') and r BiocStyle::CRANpkg('roxygen2').