DOI: 10.18129/B9.bioc.SummarizedBenchmark  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SummarizedBenchmark.

Classes and methods for performing benchmark comparisons

Bioconductor version: 3.16

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")):


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HTML R Script 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
PDF   Reference Manual
Text   NEWS


biocViews Infrastructure, Software
Version 2.16.0
In Bioconductor since BioC 3.7 (R-3.5) (5 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
Suggests iCOBRA, BiocStyle, rmarkdown, knitr, magrittr, IHW, qvalue, testthat, DESeq2, edgeR, limma, tximport, readr, scRNAseq, splatter, scater, rnaseqcomp, biomaRt
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