COREGNET statistics

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COREGNET specifications

Information


Unique identifier OMICS_08511
Name COREGNET
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.18.0
Stability Stable
Requirements
methods, RColorBrewer, gplots, R(>=2.14), BiocStyle, knitr, igraph, shiny, arules
Maintained Yes

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Documentation


Maintainer


  • person_outline Rémy Nicolle <>

Publication for COREGNET

COREGNET in publications

 (3)
PMCID: 5753469
PMID: 29298685
DOI: 10.1186/s12864-017-4389-8

[…] g. ). when multiple probes were annotating the same extracted genes that are extracted, the signals were averaged., after extracting 3615 genes in five cell types during reprogramming, we applied the coregnet package [] to infer the activity of transcription factor (tf) in the reprogramming process. the coregnet infers cooperative tf network and scores tf influences with the h-licorn algorithm by […]

PMCID: 5554221
PMID: 28955503
DOI: 10.1038/s41540-017-0024-1

[…] c/n ratio) was modulated at a constant rate), at 26 different time points, for three biological replicates. the data for 6539 genes were normalized (see materials and methods) then processed by coregnet (bioconductor package) to produce a genome-wide regulatory network. briefly, coregnet is a workflow that use the h-licorn algorithm to mine candidates grns set of co-activators […]

PMCID: 4674863
PMID: 26679516
DOI: 10.1186/1752-0509-9-S6-S6

[…] than t millions., to apply our methodology to real data, we use two different inference methods., licorn. the first one, named hlicorn, corresponds to the licorn model and is available in the coregnet bioconductor package []. in a first step, it efficiently searches the discretized gene expression matrix for sets of co-activators and co-repressors by frequent items search techniques […]


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COREGNET institution(s)
iSSB, CNRS, University of Evry, Genopole, Evry, France

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