DOI: 10.18129/B9.bioc.SummarizedBenchmark    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see SummarizedBenchmark.

Classes and methods for performing benchmark comparisons

Bioconductor version: 3.9

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 <alejandro.reyes.ds at>, Patrick Kimes <patrick.kimes at>

Maintainer: Alejandro Reyes <alejandro.reyes.ds at>, Patrick Kimes <patrick.kimes at>

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


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HTML R Script Benchmarking with SummarizedBenchmark
HTML R Script Case Study: Benchmarking Methods Not Written in R
HTML R Script Case Study: Single-Cell RNA-Seq Simulation
HTML R Script Data objects and non-standard use.
PDF   Reference Manual


biocViews Infrastructure, Software
Version 2.2.3
In Bioconductor since BioC 3.7 (R-3.5) (1.5 years)
License GPL (>= 3)
Depends R (>= 3.5), tidyr, SummarizedExperiment, S4Vectors, BiocGenerics, methods, UpSetR, rlang, stringr, utils, BiocParallel, ggplot2, mclust, dplyr, digest, sessioninfo, crayon, tibble
Suggests iCOBRA, BiocStyle, knitr, magrittr, IHW, qvalue, testthat, DESeq2, edgeR, limma, tximport, readr, scRNAseq, splatter, scater, rnaseqcomp, biomaRt
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