HDCytoData

DOI: 10.18129/B9.bioc.HDCytoData    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see HDCytoData.

Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats

Bioconductor version: 3.11

Data package containing a set of publicly available high-dimensional cytometry benchmark datasets, formatted into SummarizedExperiment and flowSet Bioconductor object formats, including all required metadata. Row metadata includes sample IDs, group IDs, patient IDs, reference cell population or cluster labels (where available), and labels identifying 'spiked in' cells (where available). Column metadata includes channel names, protein marker names, and protein marker classes (cell type or cell state).

Author: Lukas M. Weber [aut, cre], Charlotte Soneson [aut]

Maintainer: Lukas M. Weber <lukas.weber.edu at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("HDCytoData")

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("HDCytoData")

 

HTML	R Script	1. HDCytoData package
HTML	R Script	2. Examples and use cases
HTML	R Script	3. Contribution guidelines
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ExperimentData, ExperimentHub, ExpressionData, FlowCytometryData, Homo_sapiens_Data, ImmunoOncologyData, SingleCellData
Version	1.8.0
License	MIT + file LICENSE
Depends	ExperimentHub, SummarizedExperiment, flowCore
Imports	utils, methods
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM, mclust, diffcyt
SystemRequirements
Enhances
URL	https://github.com/lmweber/HDCytoData
BugReports	https://github.com/lmweber/HDCytoData/issues
Depends On Me	cytofWorkflow
Imports Me
Suggests Me	diffcyt
Links To Me
Build Report

Package Archives

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

Source Package	HDCytoData_1.8.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/HDCytoData
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HDCytoData
Package Short Url	https://bioconductor.org/packages/HDCytoData/
Package Downloads Report	Download Stats