SummarizedBenchmark

DOI: 10.18129/B9.bioc.SummarizedBenchmark    

Classes and methods for performing benchmark comparisons

Bioconductor version: Release (3.14)

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>

Installation

To install this package, start R (version "4.1") and enter:

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

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")

 

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

Details

biocViews	Infrastructure, Software
Version	2.12.0
In Bioconductor since	BioC 3.7 (R-3.5) (4 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
LinkingTo
Suggests	iCOBRA, BiocStyle, rmarkdown, knitr, magrittr, IHW, qvalue, testthat, DESeq2, edgeR, limma, tximport, readr, scRNAseq, splatter, scater, rnaseqcomp, biomaRt
SystemRequirements
Enhances
URL	https://github.com/areyesq89/SummarizedBenchmark http://bioconductor.org/packages/SummarizedBenchmark/
BugReports	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_2.12.0.tar.gz
Windows Binary	SummarizedBenchmark_2.12.0.zip
macOS 10.13 (High Sierra)	SummarizedBenchmark_2.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SummarizedBenchmark
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SummarizedBenchmark
Package Short Url	https://bioconductor.org/packages/SummarizedBenchmark/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive