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NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference.
BMC Bioinformatics ; 16: 312, 2015 Sep 29.
Artigo em Inglês | MEDLINE | ID: mdl-26415849
ABSTRACT

BACKGROUND:

In the last decade, a great number of methods for reconstructing gene regulatory networks from expression data have been proposed. However, very few tools and datasets allow to evaluate accurately and reproducibly those methods. Hence, we propose here a new tool, able to perform a systematic, yet fully reproducible, evaluation of transcriptional network inference methods.

RESULTS:

Our open-source and freely available Bioconductor package aggregates a large set of tools to assess the robustness of network inference algorithms against different simulators, topologies, sample sizes and noise intensities.

CONCLUSIONS:

The benchmarking framework that uses various datasets highlights the specialization of some methods toward network types and data. As a result, it is possible to identify the techniques that have broad overall performances.
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Texto completo: Disponível Coleções: Bases de dados internacionais Base de dados: MEDLINE Assunto principal: Software / Redes Reguladoras de Genes Limite: Humanos Idioma: Inglês Revista: BMC Bioinformatics Assunto da revista: Informática Médica Ano de publicação: 2015 Tipo de documento: Artigo País de afiliação: Espanha