SummarizedBenchmark
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.20 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see SummarizedBenchmark.
Classes and methods for performing benchmark comparisons
Bioconductor version: Release (3.20)
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("SummarizedBenchmark")):
Installation
To install this package, start R (version "4.4") 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
| Reference Manual |
Details
| biocViews | Infrastructure, Software |
| Version | 2.24.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6.5 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 | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| 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 |