SummarizedBenchmark

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see SummarizedBenchmark.

Classes and methods for performing benchmark comparisons


Bioconductor version: 3.7

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 "3.5") 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")
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. HTML R Script
Reference Manual PDF

Details

biocViews Infrastructure, Software
Version 1.0.4
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL (>= 3)
Depends R (>= 3.5), tidyr, SummarizedExperiment, S4Vectors, BiocGenerics, methods, UpSetR, rlang, stringr, utils, BiocParallel, ggplot2, mclust, dplyr
Imports
System Requirements
URL
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Suggests iCOBRA, BiocStyle, 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
Links To Me
Build Report Build Report

Package Archives

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

Source Package SummarizedBenchmark_1.0.4.tar.gz
Windows Binary SummarizedBenchmark_1.0.4.zip
Mac OS X 10.11 (El Capitan) SummarizedBenchmark_1.0.4.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
Old Source Packages for BioC 3.7 Source Archive