Package: BioNERO
Type: Package
Title: Biological Network Reconstruction Omnibus
Version: 1.19.0
Authors@R: c(person("Fabricio", "Almeida-Silva", 
                    email="fabricio_almeidasilva@hotmail.com", 
                    role=c("cre", "aut"), 
                    comment = c(ORCID = "0000-0002-5314-2964")),
            person("Thiago", "Venancio", 
            role="aut", 
            comment = c(ORCID = "0000-0002-2215-8082")))
Description: 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.
Depends: R (>= 4.1)
License: GPL-3
Encoding: UTF-8
LazyData: false
URL: https://github.com/almeidasilvaf/BioNERO
BugReports: https://github.com/almeidasilvaf/BioNERO/issues
biocViews: Software, GeneExpression, GeneRegulation, SystemsBiology,
        GraphAndNetwork, Preprocessing, Network, NetworkInference
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
RoxygenNote: 7.3.2
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle, DESeq2,
        networkD3, covr
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/pak/sysreqs: libglpk-dev make libicu-dev libpng-dev libxml2-dev
        libssl-dev perl zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:07:25 UTC
RemoteUrl: https://github.com/bioc/BioNERO
RemoteRef: HEAD
RemoteSha: 632a85bd7290a4114c61f206e49e20017323876d
NeedsCompilation: no
Packaged: 2025-11-02 14:46:59 UTC; root
Author: Fabricio Almeida-Silva [cre, aut] (ORCID:
    <https://orcid.org/0000-0002-5314-2964>),
  Thiago Venancio [aut] (ORCID: <https://orcid.org/0000-0002-2215-8082>)
Maintainer: Fabricio Almeida-Silva <fabricio_almeidasilva@hotmail.com>
Built: R 4.6.0; ; 2025-11-02 14:50:15 UTC; windows
