Abstract
Currently, standard network analysis workflows rely on many different packages, often requiring users to have a solid statistics and programming background. Here, we present BioNERO, an R package that aims to integrate all aspects of network analysis workflows, including expression data preprocessing, gene coexpression and regulatory network inference, functional analyses, and intraspecies and interspecies network comparisons. The state-of-the-art methods implemented in BioNERO ensure that users can perform all analyses with a single package in a simple pipeline, without needing to learn a myriad of package-specific syntaxes. BioNERO offers a user-friendly framework that can be easily incorporated in systems biology pipelines.
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Availability and implementation
The package is available at Bioconductor (http://bioconductor.org/packages/BioNERO).
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Funding
This work was supported by Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ; grants E-26/203.309/2016 and E-26/203.014/2018), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—Brasil (CAPES; Finance Code 001), and Conselho Nacional de Desenvolvimento Científico e Tecnológico. The funding agencies had no role in the design of the study and collection, analysis, and interpretation of data and in writing.
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Almeida-Silva, F., Venancio, T.M. BioNERO: an all-in-one R/Bioconductor package for comprehensive and easy biological network reconstruction. Funct Integr Genomics 22, 131–136 (2022). https://doi.org/10.1007/s10142-021-00821-9
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DOI: https://doi.org/10.1007/s10142-021-00821-9