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Using R and Bioconductor in Clinical Genomics and Transcriptomics

Sepulveda, Jorge L.

The Journal of molecular diagnostics : JMD, 2020-01, Vol.22 (1), p.3-20 [Periódico revisado por pares]

United States: Elsevier Inc

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  • Título:
    Using R and Bioconductor in Clinical Genomics and Transcriptomics
  • Autor: Sepulveda, Jorge L.
  • Assuntos: Computational Biology - methods ; Gene Expression Profiling - methods ; Genomics - methods ; High-Throughput Nucleotide Sequencing ; Humans ; Programming Languages ; Reproducibility of Results ; Software ; Transcriptome ; Workflow
  • É parte de: The Journal of molecular diagnostics : JMD, 2020-01, Vol.22 (1), p.3-20
  • Notas: ObjectType-Article-2
    SourceType-Scholarly Journals-1
    ObjectType-Feature-3
    content type line 23
    ObjectType-Review-1
  • Descrição: Bioinformatics pipelines are essential in the analysis of genomic and transcriptomic data generated by next-generation sequencing (NGS). Recent guidelines emphasize the need for rigorous validation and assessment of robustness, reproducibility, and quality of NGS analytic pipelines intended for clinical use. Software tools written in the R statistical language and, in particular, the set of tools available in the Bioconductor repository are widely used in research bioinformatics; and these frameworks offer several advantages for use in clinical bioinformatics, including the breath of available tools, modular nature of software packages, ease of installation, enforcement of interoperability, version control, and short learning curve. This review provides an introduction to R and Bioconductor software, its advantages and limitations for clinical bioinformatics, and illustrative examples of tools that can be used in various steps of NGS analysis.
  • Editor: United States: Elsevier Inc
  • Idioma: Inglês
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  • Realização: ABCD-USP USP   Logos de Redes Sociais: Freepik

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