NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference

[摘要] BackgroundIn 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.ResultsOur 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.ConclusionsThe 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.

[发布日期] 2015-09-29

[关键词] Bioconductor package;Gene regulatory networks;Gene expression;Gene regulation network reconstruction;Synthetic genetic networks;Benchmark