SummarizedBenchmark

DOI: 10.18129/B9.bioc.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 (3.9)

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 gmail.com>, Patrick Kimes <patrick.kimes at gmail.com>

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

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("SummarizedBenchmark", version = "3.9")

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 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

Details

biocViews Infrastructure, Software
Version 2.1.0
License GPL (>= 3)
Depends R (>= 3.5), tidyr, SummarizedExperiment, S4Vectors, BiocGenerics, methods, UpSetR, rlang, stringr, utils, BiocParallel, ggplot2, mclust, dplyr, digest, sessioninfo, crayon, tibble
Imports
LinkingTo
Suggests iCOBRA, BiocStyle, knitr, magrittr, IHW, qvalue, testthat, DESeq2, edgeR, limma, tximport, readr, scRNAseq, splatter, scater, rnaseqcomp, biomaRt
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package SummarizedBenchmark_2.1.0.tar.gz
Windows Binary SummarizedBenchmark_2.1.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) SummarizedBenchmark_2.1.0.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 http://bioconductor.org/packages/SummarizedBenchmark/
Package Downloads Report Download Stats

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