Reproducible and replicable comparisons using SummarizedBenchmark

Bioinformatics. 2019 Jan 1;35(1):137-139. doi: 10.1093/bioinformatics/bty627.


Summary: Benchmark studies are widely used to compare and evaluate tools developed for answering various biological questions. Despite the popularity of these comparisons, the implementation is often ad hoc, with little consistency across studies. To address this problem, we developed SummarizedBenchmark, an R package and framework for organizing and structuring benchmark comparisons. SummarizedBenchmark defines a general grammar for benchmarking and allows for easier setup and execution of benchmark comparisons, while improving the reproducibility and replicability of such comparisons. We demonstrate the wide applicability of our framework using four examples from different applications.

Availability and implementation: SummarizedBenchmark is an R package available through Bioconductor (

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Computational Biology / methods*
  • Reproducibility of Results
  • Software*