SummarizedBenchmark

DOI: 10.18129/B9.bioc.SummarizedBenchmark    

This is the development version of SummarizedBenchmark; to use it, please install the devel version of Bioconductor.

Classes and methods for performing benchmark comparisons

Bioconductor version: Development (3.10)

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 "3.6") and enter:

if (!requireNamespace("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")

 

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 2.3.5
In Bioconductor since BioC 3.7 (R-3.5) (1 year)
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, 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_2.3.5.tar.gz
Windows Binary SummarizedBenchmark_2.3.5.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) SummarizedBenchmark_2.3.5.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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