Reproducible and replicable comparisons using SummarizedBenchmark.

Abstract

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. SummarizedBenchmark is an R package available through Bioconductor (http://bioconductor.org/packages/SummarizedBenchmark). Supplementary data are available at Bioinformatics online.