SummarizedBenchmark

This is the development version of SummarizedBenchmark; for the stable release version, see SummarizedBenchmark.

Classes and methods for performing benchmark comparisons

Bioconductor version: Development (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 gmail.com>

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

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SummarizedBenchmark")

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

Documentation

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

browseVignettes("SummarizedBenchmark")

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
NEWS	Text

Details

biocViews	Infrastructure, Software
Version	2.19.0
In Bioconductor since	BioC 3.7 (R-3.5) (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
Imports
Linking To
Suggests	iCOBRA, BiocStyle, rmarkdown, knitr, magrittr, IHW, qvalue, testthat, DESeq2, edgeR, limma, tximport, readr, scRNAseq, splatter, scater, rnaseqcomp, biomaRt
System Requirements
Enhances
URL	https://github.com/areyesq89/SummarizedBenchmark http://bioconductor.org/packages/SummarizedBenchmark/
Bug Reports	https://github.com/areyesq89/SummarizedBenchmark/issues

Depends On Me
Imports Me
Suggests Me	benchmarkfdrData2019
Links To Me
Build Report

Package Archives

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

Source Package	SummarizedBenchmark_2.19.0.tar.gz
Windows Binary	SummarizedBenchmark_2.19.0.zip
macOS Binary (x86_64)	SummarizedBenchmark_2.19.0.tgz
macOS Binary (arm64)	SummarizedBenchmark_2.19.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SummarizedBenchmark
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SummarizedBenchmark
Bioc Package Browser	https://code.bioconductor.org/browse/SummarizedBenchmark/
Package Short Url	https://bioconductor.org/packages/SummarizedBenchmark/
Package Downloads Report	Download Stats