SummarizedBenchmark
This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see SummarizedBenchmark.
Classes and methods for performing benchmark comparisons
Bioconductor version: 3.15
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 "4.2") 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")| 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 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Infrastructure, Software |
| Version | 2.14.0 |
| 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 |
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 | benchmarkfdrData2019 |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SummarizedBenchmark_2.14.0.tar.gz |
| Windows Binary | SummarizedBenchmark_2.14.0.zip |
| macOS Binary (x86_64) | SummarizedBenchmark_2.14.0.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 3.15 | Source Archive |