CellBench

DOI: 10.18129/B9.bioc.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 (3.11)

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 "4.0") and enter:

if (!requireNamespace("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")

 

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 1.3.1
In Bioconductor since BioC 3.9 (R-3.6) (0.5 years)
License GPL-3
Depends R (>= 3.6), SingleCellExperiment, magrittr, methods, stats, tibble, utils
Imports BiocFileCache, BiocParallel, dplyr, rlang, glue, memoise, purrr (>= 0.3.0), rappdirs, tidyr, 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
Links To Me
Build Report  

Package Archives

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

Source Package CellBench_1.3.1.tar.gz
Windows Binary CellBench_1.3.0.zip
Mac OS X 10.11 (El Capitan) CellBench_1.3.1.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

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