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

Bioconductor version: Release (3.19)

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 <lmweberedu at>

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


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews ExperimentData, ExperimentHub, ExpressionData, FlowCytometryData, Homo_sapiens_Data, ImmunoOncologyData, SingleCellData
Version 1.24.0
License MIT + file LICENSE
Depends ExperimentHub, SummarizedExperiment, flowCore
Imports utils, methods
System Requirements
Bug Reports
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Suggests BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM, mclust
Linking To
Depends On Me cytofWorkflow
Imports Me
Suggests Me CytoMDS, diffcyt
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package HDCytoData_1.24.0.tar.gz
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