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>

Citation (from within R, enter citation("CellBench")):

Installation

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

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Infrastructure, Software
Version	1.8.0
In Bioconductor since	BioC 3.9 (R-3.6) (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
System Requirements
URL	https://github.com/shians/cellbench
Bug Reports	https://github.com/Shians/CellBench/issues

Suggests	BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	corral
Links To Me
Build Report	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
Bioc Package Browser	https://code.bioconductor.org/browse/CellBench/
Package Short Url	https://bioconductor.org/packages/CellBench/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.13	Source Archive