BenchHub
This is the development version of BenchHub; to use it, please install the devel version of Bioconductor.
Comprehensive Collection of Curated Benchmarking Datasets and their Evaluation
Bioconductor version: Development (3.24)
The trio is the combination of a data set, a metric and supporting evidence which provides some best case scenario, if not the ground truth itself. BenchHub has data downloaders for FigShare, G.E.O., and ExperimentHub. Caching is used to avoid lengthy downloads after the first time a data set is accessed. The user may also specify their own data set and supporting evidence. The Benchmark Insights module provides functionality for comparing and contrasting the performance of alternative algorithms.
Author: Cabiria Liang [aut], Sanghyun Kim [aut], Nick Robertson [aut], Marni Torkel [aut], Yue Cao [aut]
, Dario Strbenac [aut], Jean Yang [aut], SOMS Maintainer [aut, cre]
Maintainer: SOMS Maintainer <maths.bioconductor at sydney.edu.au>
citation("BenchHub")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("BenchHub")
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("BenchHub")| 1 Introduction to the Trio Class | HTML | R Script |
| 2 Evaluation using Trio | HTML | R Script |
| 3 Introduction of BenchmarkInsights class | HTML | R Script |
| 5 Benchmark Study | HTML | R Script |
| v04_uploading_a_Trio.html | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, DataRepresentation, Infrastructure, Software, Visualization, WorkflowStep |
| Version | 0.99.15 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | cli, fs, glue, R6, rlang, httr2, stringr, purrr, dplyr, reshape2, utils, curl, googlesheets4, survAUC, Hmisc, ggrepel, ggsci, ggcorrplot, broom, dotwhisker, splitTools, magrittr, withr, ggplot2, data.table, jsonlite |
| System Requirements | |
| URL | https://sydneybiox.github.io/BenchHub/ |
| Bug Reports | https://github.com/SydneyBioX/BenchHub/issues |
See More
| Suggests | anndata, readr, GEOquery, ExperimentHub, zen4R, knitr, ks, rmarkdown, SingleCellExperiment, SummarizedExperiment, survival, cvTools, funkyheatmap, testthat (>= 3.0.0), clusterProfiler, DOSE, DO.db, EnsDb.Hsapiens.v86, BiocStyle, tidyverse, glmnet, scran, scuttle, edgeR |
| 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 | BenchHub_0.99.15.tar.gz |
| Windows Binary (x86_64) | BenchHub_0.99.15.zip |
| macOS Binary (big-sur-x86_64) | BenchHub_0.99.15.tgz |
| macOS Binary (sonoma-arm64) | BenchHub_0.99.15.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BenchHub |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BenchHub |
| Bioc Package Browser | https://code.bioconductor.org/browse/BenchHub/ |
| Package Short Url | https://bioconductor.org/packages/BenchHub/ |
| Package Downloads Report | Download Stats |