Registration and Call for Abstracts Open for Bioc2024


Classes and methods for performing benchmark comparisons

Bioconductor version: Release (3.18)

This package defines the BenchDesign and SummarizedBenchmark classes for building, executing, and evaluating benchmark experiments of computational methods. The SummarizedBenchmark class extends the RangedSummarizedExperiment object, and is designed to provide infrastructure to store and compare the results of applying different methods to a shared data set. This class provides an integrated interface to store metadata such as method parameters and software versions as well as ground truths (when these are available) and evaluation metrics.

Author: Alejandro Reyes [aut] , Patrick Kimes [aut, cre]

Maintainer: Patrick Kimes <patrick.kimes at>

Citation (from within R, enter citation("SummarizedBenchmark")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Case Study: Benchmarking non-R Methods HTML R Script
Case Study: Single-Cell RNA-Seq Simulation HTML R Script
Feature: Error Handling HTML R Script
Feature: Iterative Benchmarking HTML R Script
Feature: Parallelization HTML R Script
SummarizedBenchmark: Class Details HTML R Script
SummarizedBenchmark: Full Case Study HTML R Script
SummarizedBenchmark: Introduction HTML R Script
Reference Manual PDF


biocViews Infrastructure, Software
Version 2.20.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL (>= 3)
Depends R (>= 3.6), tidyr, SummarizedExperiment, S4Vectors, BiocGenerics, methods, UpSetR, rlang, stringr, utils, BiocParallel, ggplot2, mclust, dplyr, digest, sessioninfo, crayon, tibble
System Requirements
Bug Reports
See More
Suggests iCOBRA, BiocStyle, rmarkdown, knitr, magrittr, IHW, qvalue, testthat, DESeq2, edgeR, limma, tximport, readr, scRNAseq, splatter, scater, rnaseqcomp, biomaRt
Linking To
Depends On Me
Imports Me
Suggests Me benchmarkfdrData2019
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SummarizedBenchmark_2.20.0.tar.gz
Windows Binary
macOS Binary (x86_64) SummarizedBenchmark_2.20.0.tgz
macOS Binary (arm64) SummarizedBenchmark_2.20.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats