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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 (3.19)

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 "4.4") 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 2.21.0
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
Imports
System Requirements
URL https://github.com/areyesq89/SummarizedBenchmark http://bioconductor.org/packages/SummarizedBenchmark/
Bug Reports https://github.com/areyesq89/SummarizedBenchmark/issues
See More
Suggests iCOBRA, BiocStyle, rmarkdown, knitr, magrittr, IHW, qvalue, testthat, DESeq2, edgeR, limma, tximport, readr, scRNAseq, splatter, scater, rnaseqcomp, biomaRt
Linking To
Enhances
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_2.21.0.tar.gz
Windows Binary SummarizedBenchmark_2.21.0.zip
macOS Binary (x86_64) SummarizedBenchmark_2.21.0.tgz
macOS Binary (arm64) SummarizedBenchmark_2.21.0.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