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minet specifications

Information


Unique identifier OMICS_10584
Name minet
Alternative name Mutual Information NETworks
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 3.38.0
Stability Stable
Requirements
infotheo
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Patrick Meyer

Publication for Mutual Information NETworks

minet citations

 (21)
call_split

Genetic Architecture and Candidate Genes Identified for Follicle Number in Chicken

2017
Sci Rep
PMCID: 5703906
PMID: 29180824
DOI: 10.1038/s41598-017-16557-1
call_split See protocol

[…] t Effect Predictor (VEP) and BioMart tools were performed to identify the candidate genes that located the significant SNPs,. A mutual information network was generated based on current results using minet package for R with the Aracne algorithm. The network graphs were exported from R for visualization in the MCODE package within Cytoscape 3.2.1,. Using this visualization tool, we explored networ […]

library_books

Estimation of the proteomic cancer co expression sub networks by using association estimators

2017
PLoS One
PMCID: 5690670
PMID: 29145449
DOI: 10.1371/journal.pone.0188016

[…] For the analyses, the build.mim function from the minet [], the obtain.mim function from the DepEst [] and the chooseOneHubInEachModule, adjacency, TOMsimilarity, cutreeDynamic and hclust functions from the WGCNA packages were used. The selected asso […]

library_books

Plasma and Serum Metabolite Association Networks: Comparability within and between Studies Using NMR and MS Profiling

2017
J Proteome Res
PMCID: 5645760
PMID: 28517934
DOI: 10.1021/acs.jproteome.7b00106

[…] triplet is interpreted as an indirect interaction and is removed if the difference between the two lowest weights is above a threshold γ. We used the ARANCE implementation presented in the R package “minet” with default parameters (γ = 0). […]

library_books

Enlightening discriminative network functional modules behind Principal Component Analysis separation in differential omic science studies

2017
Sci Rep
PMCID: 5347127
PMID: 28287094
DOI: 10.1038/srep43946

[…] neral such as PC-corr does. Network reconstruction techniques can be generally divided into two broad classes: biological knowledge-driven (such as STRING) or data-driven (such as the above-mentioned minet, which for instance can be applied to expression data). However, both these methods only focus on the features’ interactions, neglecting their role in discriminating two or multiple conditions, […]

library_books

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

2016
F1000Res
PMCID: 5302158
PMID: 28232861
DOI: 10.5256/f1000research.9601.r14695

[…] yer _ 1.32.1 22 [5] motifStack _ 1.16.2 23 [6] ade4 _ 1.7–4 24 [7] grImport _ 0.9–0 25 [8] XML _ 3.98–1.4 26 [9] MotIV _ 1.28.0 27 [10] pathview _ 1.12.0 28 [11] biomaRt _ 2.28.0 29 [12] minet _ 3.30.0 30 [13] clusterProfiler _ 3.0.4 31 [14] DOSE _ 2.10.7 32 [15] AnnotationHub _ 2.4.2 33 [16] ChIPseeker _ 1.8.7 34 [17] ELMER _ 1.4.2 35 [18] ELMER. data_ 1.2.2 36 [19] Homo.sapie […]

call_split

Heat Stress and Lipopolysaccharide Stimulation of Chicken Macrophage Like Cell Line Activates Expression of Distinct Sets of Genes

2016
PLoS One
PMCID: 5063343
PMID: 27736938
DOI: 10.1371/journal.pone.0164575
call_split See protocol

[…] WGCNA package for R [] with Spearman correlation threshold of 0.8 determined based on the density plot. Additionally, a mutual information network was generated from LMH transcriptomic data [] using minet package for R [] with the Aracne algorithm. The network graphs were exported from R for visualization in Cytoscape 3.2.1 []. Network clustering was performed on graphs from this study with the M […]

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minet institution(s)
Machine Learning Group, Computer Science Department, Faculty of Science, Université Libre de Bruxelles, Brussels, Belgium
minet funding source(s)
This work was partially funded by the Communauté Française de Belgique under ARC grant no. 04/09-307.

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