Registration Open for Bioc2024 July 24-26


Biological Network Reconstruction Omnibus

Bioconductor version: Release (3.19)

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>

Citation (from within R, enter citation("BioNERO")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews GeneExpression, GeneRegulation, GraphAndNetwork, Network, NetworkInference, Preprocessing, Software, SystemsBiology
Version 1.12.0
In Bioconductor since BioC 3.13 (R-4.1) (3 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
System Requirements
Bug Reports
See More
Suggests knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle, DESeq2, networkD3, covr
Linking To
Depends On Me
Imports Me cageminer
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BioNERO_1.12.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) BioNERO_1.12.0.tgz
macOS Binary (arm64) BioNERO_1.12.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats