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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "BioNERO" in publications use:'
type: software
license: GPL-3.0-only
title: 'BioNERO: Biological Network Reconstruction Omnibus'
version: 1.13.0
doi: 10.1007/s10142-021-00821-9
abstract: 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.
authors:
- family-names: Almeida-Silva
  given-names: Fabricio
  email: fabricio_almeidasilva@hotmail.com
  orcid: https://orcid.org/0000-0002-5314-2964
- family-names: Venancio
  given-names: Thiago
  orcid: https://orcid.org/0000-0002-2215-8082
preferred-citation:
  type: article
  title: 'BioNERO: an all-in-one R/Bioconductor package for comprehensive and easy
    biological network reconstruction'
  authors:
  - family-names: Almeida-Silva
    given-names: Fabricio
    email: fabricio_almeidasilva@hotmail.com
    orcid: https://orcid.org/0000-0002-5314-2964
  - family-names: Venancio
    given-names: Thiago M.
  journal: Functional And Integrative Genomics
  year: '2022'
  volume: '22'
  issue: '1'
  url: https://link.springer.com/article/10.1007/s10142-021-00821-9
  doi: 10.1007/s10142-021-00821-9
  start: 131-136
repository: https://bioc.r-universe.dev
repository-code: https://github.com/almeidasilvaf/BioNERO
url: https://github.com/almeidasilvaf/BioNERO
contact:
- family-names: Almeida-Silva
  given-names: Fabricio
  email: fabricio_almeidasilva@hotmail.com
  orcid: https://orcid.org/0000-0002-5314-2964