Package: magrene 1.9.0

Fabrício Almeida-Silva

magrene: Motif Analysis In Gene Regulatory Networks

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.

Authors:Fabrício Almeida-Silva [aut, cre], Yves Van de Peer [aut]

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NEWS

# Install 'magrene' in R:
install.packages('magrene', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/almeidasilvaf/magrene/issues

Datasets:
  • gma_grn - Sample soybean GRN
  • gma_paralogs - Soybean (Glycine max) duplicated genes
  • gma_ppi - Sample soybean PPI network
  • nulls - Null distribution of motif frequencies for vignette data set

On BioConductor:magrene-1.9.0(bioc 3.21)magrene-1.8.0(bioc 3.20)

softwaremotifdiscoverynetworkenrichmentsystemsbiologygraphandnetworkgene-regulatory-networkmotif-analysisnetwork-motifsnetwork-science

4.00 score 1 stars 2 scripts 149 downloads 8 exports 9 dependencies

Last updated 2 months agofrom:99513a8f0c. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-winNOTEDec 18 2024
R-4.5-linuxNOTEDec 18 2024
R-4.4-winNOTEDec 18 2024
R-4.4-macNOTEDec 18 2024
R-4.3-winOKDec 18 2024
R-4.3-macOKDec 18 2024

Exports:calculate_Zfind_bifanfind_deltafind_lambdafind_ppi_vfind_vgenerate_nullssd_similarity

Dependencies:BHBiocParallelcodetoolscpp11formatRfutile.loggerfutile.optionslambda.rsnow

Introduction to magrene

Rendered frommagrene.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2022-08-26
Started: 2022-01-21