title: NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference.
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.
authors.affiliation: Universitat Politecnica de Catalunya BarcelonaTECH, Department of Signal Theory and Communications, UPC-Campus Nord, C/ Jordi Girona, 1-3, Barcelona, 08034, Spain. pau.bellot@upc.edu.|Bioinformatics and Systems Biology (BioSys), Faculty of Sciences, Université de Liège (ULg), 27 Blvd du Rectorat, Liège, 4000, Belgium. pau.bellot@upc.edu.
authors.forename: Pau
authors.initials: P
authors.lastname: Bellot
authors.affiliation: Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium. colsen@ulb.ac.be.|Interuniversity Institute of Bioinformatics Brussels, (IB)², Brussels, Belgium. colsen@ulb.ac.be.
authors.forename: Catharina
authors.initials: C
authors.lastname: Olsen
authors.affiliation: Universitat Politecnica de Catalunya BarcelonaTECH, Department of Signal Theory and Communications, UPC-Campus Nord, C/ Jordi Girona, 1-3, Barcelona, 08034, Spain. philippe.salembier@upc.edu.
authors.forename: Philippe
authors.initials: P
authors.lastname: Salembier
authors.affiliation: Universitat Politecnica de Catalunya BarcelonaTECH, Department of Signal Theory and Communications, UPC-Campus Nord, C/ Jordi Girona, 1-3, Barcelona, 08034, Spain. albert.oliveras@upc.edu.
authors.forename: Albert
authors.initials: A
authors.lastname: Oliveras-Vergés
authors.affiliation: Bioinformatics and Systems Biology (BioSys), Faculty of Sciences, Université de Liège (ULg), 27 Blvd du Rectorat, Liège, 4000, Belgium. patrick.meyer@ulg.ac.be.
authors.forename: Patrick E
authors.initials: PE
authors.lastname: Meyer
mesh_terms: D000465:Algorithms; D019540:Area Under Curve; D019985:Benchmarking; D053263:Gene Regulatory Networks; D006801:Humans; D012372:ROC Curve; D012984:Software