期刊
BMC BIOINFORMATICS
卷 16, 期 -, 页码 -出版社
BMC
DOI: 10.1186/s12859-015-0728-4
关键词
Bioconductor package; Gene regulatory networks; Gene expression; Gene regulation network reconstruction; Synthetic genetic networks; Benchmark
类别
资金
- Spanish Ministerio de Educacion
- Cultura y Deporte FPU Research Fellowship
- Cellex foundation
- Innoviris EHealth platform project BridgeIris
- ULB postdoctoral position
- Spanish Ministerio de Economia y Competitividad
- European Regional Development Fund (ERDF)
- University of Liege [SFRD-12/03, SFRD-12/04, C-14/73]
- Credit de Recherche of the FNRS [23678785]
- [BIGGRAPH-TEC2013-43935-R]
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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