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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.    Electronic supplementary material  The online version of this article (doi:10.1186/s12859-015-0728-4) contains supplementary material, which is available to authorized users.

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