DOI: 10.18129/B9.bioc.BioNERO  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see BioNERO.

Biological Network Reconstruction Omnibus

Bioconductor version: 3.17

BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses for biological interpretations. BioNERO can be used to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs) from gene expression data. Additionally, it can be used to explore topological properties of protein-protein interaction (PPI) networks. GCN inference relies on the popular WGCNA algorithm. GRN inference is based on the "wisdom of the crowds" principle, which consists in inferring GRNs with multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average rank for each interaction pair. As all steps of network analyses are included in this package, BioNERO makes users avoid having to learn the syntaxes of several packages and how to communicate between them. Finally, users can also identify consensus modules across independent expression sets and calculate intra and interspecies module preservation statistics between different networks.

Author: Fabricio Almeida-Silva [cre, aut] , Thiago Venancio [aut]

Maintainer: Fabricio Almeida-Silva <fabricio_almeidasilva at>

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HTML R Script Gene coexpression network inference
HTML R Script Gene regulatory network inference with BioNERO
HTML R Script Network comparison: consensus modules and module preservation
PDF   Reference Manual
Text   NEWS


biocViews GeneExpression, GeneRegulation, GraphAndNetwork, Network, NetworkInference, Preprocessing, Software, SystemsBiology
Version 1.8.7
In Bioconductor since BioC 3.13 (R-4.1) (2.5 years)
License GPL-3
Depends R (>= 4.1)
Imports WGCNA, dynamicTreeCut, ggdendro, matrixStats, sva, RColorBrewer, ComplexHeatmap, ggplot2, rlang, ggrepel, patchwork, reshape2, igraph, ggnetwork, intergraph, NetRep, stats, grDevices, utils, methods, BiocParallel, minet, GENIE3, SummarizedExperiment
Suggests knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle, DESeq2, networkD3, covr
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Imports Me cageminer
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