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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

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

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
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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