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CellBench

This is the development version of CellBench; for the stable release version, see CellBench.

Construct Benchmarks for Single Cell Analysis Methods


Bioconductor version: Development (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 (from within R, enter citation("CellBench")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews Infrastructure, SingleCell, Software
Version 1.19.0
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 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_1.19.0.tar.gz
Windows Binary CellBench_1.19.0.zip (64-bit only)
macOS Binary (x86_64) CellBench_1.19.0.tgz
macOS Binary (arm64) CellBench_1.19.0.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