CellBench
Construct Benchmarks for Single Cell Analysis Methods
Bioconductor version: Release (3.19)
This package contains infrastructure for benchmarking analysis methods and access to single cell mixture benchmarking data. It provides a framework for organising analysis methods and testing combinations of methods in a pipeline without explicitly laying out each combination. It also provides utilities for sampling and filtering SingleCellExperiment objects, constructing lists of functions with varying parameters, and multithreaded evaluation of analysis methods.
Author: Shian Su [cre, aut], Saskia Freytag [aut], Luyi Tian [aut], Xueyi Dong [aut], Matthew Ritchie [aut], Peter Hickey [ctb], Stuart Lee [ctb]
Maintainer: Shian Su <su.s at wehi.edu.au>
citation("CellBench")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CellBench")
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("CellBench")| Data Manipulation | HTML | R Script |
| Introduction | HTML | R Script |
| Tidyverse Patterns | HTML | R Script |
| Timing | HTML | R Script |
| Writing Wrappers | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Infrastructure, SingleCell, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.6), SingleCellExperiment, magrittr, methods, stats, tibble, utils |
| Imports | assertthat, BiocGenerics, BiocFileCache, BiocParallel, dplyr, rlang, glue, memoise, purrr (>= 0.3.0), rappdirs, tidyr, tidyselect, lubridate |
| System Requirements | |
| URL | https://github.com/shians/cellbench |
| Bug Reports | https://github.com/Shians/CellBench/issues |
See More
| Suggests | BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | corral, speckle |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CellBench_1.20.0.tar.gz |
| Windows Binary (x86_64) | CellBench_1.20.0.zip |
| macOS Binary (x86_64) | CellBench_1.20.0.tgz |
| macOS Binary (arm64) | CellBench_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CellBench |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CellBench |
| Bioc Package Browser | https://code.bioconductor.org/browse/CellBench/ |
| Package Short Url | https://bioconductor.org/packages/CellBench/ |
| Package Downloads Report | Download Stats |