CellBench

DOI: 10.18129/B9.bioc.CellBench    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see CellBench.

Construct Benchmarks for Single Cell Analysis Methods

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML		CellBenchCaseStudy.html
PDF	R Script	Data Manipulation
HTML	R Script	Introduction
PDF	R Script	Tidyverse Patterns
HTML	R Script	Timing
HTML	R Script	Writing Wrappers
PDF		Reference Manual
Text		NEWS

Details

biocViews	Infrastructure, Software
Version	1.8.0
In Bioconductor since	BioC 3.9 (R-3.6) (2.5 years)
License	GPL-3
Depends	R (>= 3.6), SingleCellExperiment, magrittr, methods, stats, tibble, utils
Imports	BiocGenerics, BiocFileCache, BiocParallel, dplyr, rlang, glue, memoise, purrr (>= 0.3.0), rappdirs, tidyr, tidyselect, lubridate
LinkingTo
Suggests	BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2
SystemRequirements
Enhances
URL	https://github.com/shians/cellbench
BugReports	https://github.com/Shians/CellBench/issues
Depends On Me
Imports Me
Suggests Me	corral
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	CellBench_1.8.0.tar.gz
Windows Binary	CellBench_1.8.0.zip
macOS 10.13 (High Sierra)	CellBench_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CellBench
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CellBench
Package Short Url	https://bioconductor.org/packages/CellBench/
Package Downloads Report	Download Stats